Nomenclature for the KIR of non-human species

Nomenclature for the KIR of non-human species The increasing number of Killer Immunoglobulin-like Receptor (KIR) sequences available for non-human primate species and cattle has prompted development of a centralized database, guidelines for a standardized nomenclature, and minimum require- ments for database submission. The guidelines and nomenclature are based on those used for human KIR and incorporate modifications made for inclusion of non-human species in the companion IPD-NHKIR database. Included in this first release are the rhesus macaque (Macaca mulatta), chimpanzee (Pan troglodytes), orangutan (Pongo abelii and Pongo pygmaeus), and cattle (Bos taurus). . . . . . . Keywords KIR Nomenclature Variant Allele Gene Database Sequence Introduction made it difficult to assign orthologues and have led to a num- ber of different nomenclature systems being used to name The KIR locus has been studied in a number of non-human genes and alleles. This report describes a common framework species primates and is characterized by high levels of allelic and guidelines for KIR nomenclature in non-human species. polymorphism, haplotypic polymorphism in the number of These have been developed by taking advantage of lessons genes, and extensive duplication and recombination learned in the development of a nomenclature system for the (Hammond et al. 2016; Parham 2004). These factors have human KIR (Marsh et al. 2003). General naming guidelines * Steven G. E. Marsh steven.marsh@ucl.ac.uk To provide consistency with the IPD-MHC Database (Maccari et al. 2017), the non-human KIR nomenclature Anthony Nolan Research Institute, London, UK adopts the same four-character prefix used for species desig- nation in the naming of MHC alleles (de Groot et al. 2012; UCL Cancer Institute, University College London, London, UK Ellis et al. 2006; Klein et al. 1990). Also, genes and alleles will Department of Structural Biology and Department of Microbiology be named based on the conventions that have been adopted for & Immunology, School of Medicine, Stanford University, Stanford, CA, USA the human KIR system (Marsh et al. 2003) that are based on the structures of the molecules they encode. The first digit The Pirbright Institute, Woking, UK following the KIR acronym corresponds to the number of Biomedical Primate Research Centre, Rijswijk, Netherlands Ig-like domains in the polypeptide and the BD^ denotes Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA BDomain.^ The D is followed by either an BL^ indicating a Oregon National Primate Research Centre, Oregon Health and BLong^ cytoplasmic tail, an BS^ indicating a BShort^ cytoplas- Science University, OR Beaverton, USA mic tail or a BP^ for pseudogenes. In addition, the inclusion of Nuffield Department of Clinical Medicine, University of Oxford, a BW^ indicates BWorkshop^ following the BL,^ BS,^ or BP^ to Oxford, UK indicate any sequence that by phylogenetic analysis is suffi- Aix-Marseille II University, Marseille, France ciently divergent to be considered a Bnew^ gene, but lack German Primate Centre, Gottingen, Germany either genomic sequencing or family studies to demonstrate 572 Immunogenetics (2018) 70:571–583 that it does define a new gene and not a divergent lineage a identity is known of the animal providing the sequenced known gene. Tables 1, 2,and 3 list the current gene designa- DNA, that information is included in the database, as well as tions and their previous names. Symbols for genes are itali- information regarding the origin of the animal. Tables 4, 5, 6, cized (e.g., Mamu-KIR3DL01), whereas symbols for proteins and 7 provide a complete list of genes and alleles currently in are not italicized (e.g., Mamu-KIR3DL01). Alleles follow the the nomenclature, as well as the original name(s), accession same conventions as gene names. number, and reference to the original report of the sequence. Reflecting species-specific differences, there have been Each KIR allele name includes a unique number corre- further additions/modifications to the general nomenclature sponding to up to three sets of digits separated by colons. for rhesus macaque and cattle. As with the human KIR no- All alleles are given a three-digit name, which corresponds menclature, alleles in each series have been named in order of to the first set of digits; longer names are assigned only their deposition into a generalist sequence databank, when necessary. GenBank/EMBL-ENA/DDBJ (Benson et al. 2017; The digits placed before the first colon describe the alleles Chojnacki et al. 2017; Mashima et al. 2017). Where the that differ at non-synonymous substitutions (also called coding Table 1 Gene designations and Species KIR gene Previous KIR gene designation(s) their previous names designation(s) Rhesus Mamu-KIR1D KIR1D, Mamu-KIR1D macaque Mamu-KIR2DL04 2DL501NK, 2DL503NK, KIR2DL4, KIR2DL4.1, MmKIR2DL4 (Mamu) Mamu-KIR3DL01 2DL426NK, 3DL34, KIR3DL, KIR3DL-like_1, KIR3DL1, KIR3DL1-like1, KIR3DL12, KIR3DL13, KIR3DL14, KIR3DL15, KIR3DL19, KIR3DL1_variant_2, KIR3DL2, KIR3DL2-old, KIR3DL3, KIR3DL4, KIR3DL5 Mamu-KIR3DL02 KIR3DL-like_3, KIR3DL2, KIR3DL21, KIR3DL21-like1 Mamu-KIR3DL04 KIR3DL11 Mamu-KIR3DL05 3DL7b-3DL40, KIR3DL, KIR3DL-3, KIR3DL16, KIR3DL7, KIR3DL7-like2, KIR3DL07 Mamu-KIR3DL06 KIR3DL6 Mamu-KIR3DL07 2DL420, KIR3DL, KIR3DL18, KIR3DL7, KIR3DL7-like1, KIR3DL7-like3, KIR3DL03 Mamu-KIR3DL08 KIR3DL, KIR3DL-like_2, KIR3DL17, KIR3DL8, KIRDL8, Mamu-KIR3DL04, Mamu-KIR3DL4 Mamu-KIR3DL10 3DL10-2DL501, 3DL3NK, KIR3DL, KIR3DL10, KIR3DL9, Mamu-KIR3DL05 Mamu-KIR3DL11 KIR3DL, KIR3DL-1, KIR3DL-6, KIR3DL-7, KIR3DL11 Mamu-KIR3DL20 KIR3DL20, KIR3DL20_variant_2, KIR3DL06, KIR2DL5 Mamu-KIR3DLW03 KIR3DL-4, KIR3DL-5, KIR3DL-like1-BNB, KIR3DL21 Mamu-KIR3DLX1 KIR3DL0 Mamu-KIR3DS01 KIR3DH-7, KIR3DH1, KIR3DH5, Mamu-KIR3DS01-JHB-HEFGH, Mamu-KIR3DS02 3DH2, 3DH42, KIR3DH-like_5, KIR3DH-like_6, KIR3DH10, KIR3DH12, KIR3DH13, KIR3DH14, KIR3DH15, KIR3DH16, KIR3DH2 Mamu-KIR3DS03 KIR3DH3, KIR3DH8, KIR3DH9 Mamu-KIR3DS04 KIR3DH-1, KIR3DH4, KIR3DH6 Mamu-KIR3DS05 KIR3DH1, KIR3DM-1, KIR3DM1, KIR3DM6, KIR_Partial_ Sequence_1 Mamu-KIR3DS06 KIR3DH-4, KIR3DH-like8, KIR3DH-like_7, KIR3DH18, Mamu-KIR3DSW07 KIR3DH-5, KIR3DH7, Mamu-KIR3DS07-JHB-HO Mamu-KIR3DSW08 KIR3DH-2, KIR3DH-3, KIR3DH-4, KIR3DH-5, KIR3DH-like_1, KIR3DH-like_2, KIR3DH-like_3, KIR3DH-like_4, KIR3DH21, KIR3DSW08 Mamu-KIR3DSW09 KIR3DH-8, KIR3DH20, KIR3DH5, KIR3DH5-like1, mmKIR3DH-1 Immunogenetics (2018) 70:571–583 573 Table 2 Gene designations and their previous names second sets of digits. Alleles that only differ by sequence poly- morphisms in the introns, or in the 5′ or 3′ untranslated regions Species KIR gene Previous KIR gene designation(s) that flank the exons and introns, are distinguished by their third designation(s) sets of digits. Chimpanzee Patr-KIR2DL4 In addition to the unique allele number, optional suf- (Patr) Patr-KIR2DL5 fixescan be addedtoanallelename toindicatethe ex- Patr-KIR2DL6 Pt-NewII pression status of the gene and/or its encoded protein. Patr-KIR2DL7 Alleles known not to be expressed—so called BNull^ al- Patr-KIR2DL8 Pt-NewIII leles—have been given the suffix BN.^ Alleles that have Patr-KIR2DL9 been shown to be alternatively expressed may have the Patr-KIR3DL1 Pt-KIR3DL1/2, Pt-KIR3DL3, suffix BL,^ BS,^ BC,^ BA,^ or BQ.^ Pt-KIR3DL1, Pt-KIR3DL2 The suffix BL^ is used to indicate an allele that has been Patr-KIR3DL3 Patr-KIRC1, Pt-NewI shown to have BLow^ cell surface expression when compared Patr-KIR3DL4 to normal levels. The BS^ suffix is used to denote an allele Patr-KIR3DL5 specifying a protein which is expressed as a soluble, Patr-KIR3DS6 Pt-KIR3DL6 BSecreted^ molecule and is not present on the cell surface. The BC^ suffix is assigned to alleles producing proteins that are present in the BCytoplasm^ and not on the cell surface. An substitutions). Alleles that differ only by synonymous nucleo- BA^ suffix indicates an BAberrant^ expression, where there is tide substitutions (also called silent or non-coding substitutions) doubt as to whether a protein is actually expressed. A BQ^ but are within the coding sequence are distinguished by their suffix is used when the expression of an allele is BQuestionable,^ given that the mutation seen in the allele Table 3 Gene designations and their previous names has been shown to affect normal expression levels in other alleles and other KIR genes. Species KIR gene Previous KIR gene designation(s) As of May 2018, no alleles have been named with the BC,^ designation(s) BA,^ BQ,^ or BS^ suffixes. Orangutan Poab-KIR2DL10 Popy-KIR2DL10, 2DLA A schematic representation of the syntax for the non- (Poab) Poab-KIR2DL11 Popy-KIR2DL11, 2DLB human KIR allele designation is shown in Fig. 1. Poab-KIR2DL12 Popy-KIR2DL11, 2DLC Poab-KIR2DL5 Popy-KIR2DL5. 2DL5 Species-specific guidelines Poab-KIR2DS10 2DSD/2DSA Poab-KIR2DS13 Popy-KIR2DS13, 2DSC1/2DSB Naming rhesus macaque KIR genes Poab-KIR2DS14 Popy-KIR2DS14, 2DSB/2DSD2, 2DSA/2DSD1 The Mamu-KIR sequences fall into a number of distinct Poab-KIR3DL1 Popy-KIR3DL1, 3DLH, 3DLC, lineages based on phylogenetic analysis. Most sequences 3DLD2, 3DLD1, 3DLA, 3DLI, correspond to lineage II KIR and are further divided 3DLB into those encoding KIR that have long cytoplamic tails Poab-KIR3DL3 Popy-KIR3DL3, 3DL3 or short cytoplasmic tails. The genes have been num- Poab-KIR3DS1 Popy-KIR3DS1, 3DS1 bered sequentially and where possible the gene name Poab-KIRDP Popy-KIRDP, DP has the same the same number as the first reported Orangutan Popy-KIR2DL11 Popy-KIR2DLB allele for that gene. For example, the Mamu-KIR3DL1 (Popy) Popy-KIR2DL12 Popy-KIR2DLC gene (Hershberger et al. 2001)was renamed Mamu- Popy-KIR2DL5 KIR3DL01*001. Popy-KIR2DS10 Popy-KIR2DSD/2DSA The nomenclature uses a two-digit numbering of individ- Popy-KIR2DS13 Popy-KIR2DSC2/2DSB ual genes for the macaque sequences as seen with the nam- Popy-KIR2DS14 Popy-KIR2DSB/2DSD2, ing of Mamu-KIR3DL01*001. This renaming aims to avoid 2DSA/2DSD1 confusion with previous sequence names. Subsequent anal- Popy-KIR2DS15 ysis has shown that some of the proposed sequences of dif- Popy-KIR3DL1 Popy-KIR3DL1, 3DLF, 3DLE2, ferent genes are actually allelic variants of the same gene. 3DLE1 Rather than skipping numbers to avoid confusion, it was Popy-KIR3DL3 Popy-KIR3DL3, 3DL3 thought better to introduce the two-digit numbering system. Popy-KIR3DS1 Popy-KIR3DS1, 3DS1 Recombinant alleles are named according to the locus, Popy-KIRDP Popy-KIRDP, DP which provide the majority of the sequence. For example, 574 Immunogenetics (2018) 70:571–583 Table 4 Allele designations and their previous names Gene Allele designation Previous designations Accession number Reference Mamu-KIR1D Mamu-KIR1D*001 KIR1D AF334634 (Hershberger et al. 2001) Mamu-KIR1D Mamu-KIR1D*002 KIR1D,Mamu-KIR1D*00202-JHB-HA AY728181, GU112257, (Sambrook et al. 2005) GU112266, GU112332 (Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*001:01 KIR2DL4, KIR2DL4.1, EU702486, AF361088, (Blokhuis et al. 2009a; MmKIR2DL4*0010101-JHB AF334644, FJ824091, Blokhuis et al. 2009b; GU112331, GU112318, Blokhuis et al. 2010; GU112263, GU112303, Grendell et al. 2001; GU112287 Hershberger et al. 2001) Mamu-KIR2DL04 Mamu-KIR2DL04*001:02 2DL501NK GU299490 (Colantonio et al. 2011) Mamu-KIR2DL04 Mamu-KIR2DL04*002 MmKIR2DL4*0020101-JHB FJ824092, GU112279 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*003 KIR2DL4, AY505486, FJ824093, (Andersen et al. 2004; MmKIR2DL4*0040101-JHB GU112322, GU112284 Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*004 KIR2DL4 AY728182 (Sambrook et al. 2005) Mamu-KIR2DL04 Mamu-KIR2DL04*005 MmKIR2DL4*0050101-JHB FJ824094 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*006:01 MmKIR2DL4*0060101-JHB FJ824095 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*006:02 2DL503NK GU014298 (Colantonio et al. 2011) Mamu-KIR2DL04 Mamu-KIR2DL04*007 MmKIR2DL4*0070101-JHB FJ824096 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*008:01 MmKIR2DL4*0080101-JHB FJ824097 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*008:02 MmKIR2DL4*0080201-JHB FJ824098, GU112326 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*010 MmKIR2DL4*0100101-JHB FJ824100 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*011 MmKIR2DL4*0110101-JHB FJ824101 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*012 MmKIR2DL4*0120101-JHB FJ824102 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*013 MmKIR2DL4*0130101-JHB FJ824103 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*014:01 MmKIR2DL4*0140101-JHB FJ824104, GU112316 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*014:02 MmKIR2DL4*0140201-JHB FJ824105 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*015:01 MmKIR2DL4*0150101-JHB FJ824106, GU112313 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*015:02 MmKIR2DL4*0150201-JHB FJ824107, GU112280 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*016 MmKIR2DL4*0160101-JHB FJ824108 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*017 MmKIR2DL4*0170101-JHB FJ824109 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*018 MmKIR2DL4*0180101-JHB FJ824110 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*019 MmKIR2DL4*0190101-JHB FJ824111 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*020 MmKIR2DL4*0200101-JHB FJ824112, GU112274 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*001 KIR3DL1, 3DL34 AF334616, GU299488 (Colantonio et al. 2011; Hershberger et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*002 KIR3DL2-old, 2DL426NK AF334617, GU299488 (Hershberger et al. 2001), (Colantonio et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*003 KIR3DL3 AF361083, GU112305 (Blokhuis et al. 2010; Grendell et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*004 KIR3DL4 AF334619 (Hershberger et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*005 KIR3DL5 AF334620 (Hershberger et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*006 KIR3DL12 AF361082 (Grendell et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*007N KIR3DL13 AF408151 (Grendell et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*008N KIR3DL14 AF408152 (Grendell et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*009N KIR3DL15 AF408153 (Grendell et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*010 KIR3DL19 AF408150 (Grendell et al. 2001) Immunogenetics (2018) 70:571–583 575 Table 4 (continued) Gene Allele designation Previous designations Accession number Reference Mamu-KIR3DL01 Mamu-KIR3DL01*011 KIR3DL1_variant_2 AY728187 (Sambrook et al. 2005) Mamu-KIR3DL01 Mamu-KIR3DL01*012 KIR3DL1*002-BNB, KIR3DL-like_1 EU419033, AY505476, (Andersen et al. 2004; GU112286 Blokhuis et al. 2010; Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*013 KIR3DL1*003-BNB EU419034 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*014 KIR3DL1*005-BNB EU419035 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*015 KIR3DL1*006-BNB EU419036 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*016 KIR3DL1*007-BNB EU419037, GU112258 (Blokhuis et al. 2010; Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*017 KIR3DL12*001-BNB EU419044 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*018 KIR3DL2*001-BNB EU419046 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*019:01 KIR3DL1*001-BNB EU419032, GU112300 (Blokhuis et al. 2010; Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*019:02 None GU112283 (Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*020 KIR3DL1-like1 EU688987 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*021 KIR3DL FJ562108 (Bostik et al. 2009) Mamu-KIR3DL01 Mamu-KIR3DL01*022 None GU112267 (Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*023 None GU112292 (Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*024 None GU112321 (Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*025 None GU112324 (Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*026 KIR3DL allele 2 FJ562109 (Bostik et al. 2009) Mamu-KIR3DL01 Mamu-KIR3DL01*027 KIR3DL allele 3 FJ562110 (Bostik et al. 2009) Mamu-KIR3DL02 Mamu-KIR3DL02*001 KIR3DL2 AY728188 (Sambrook et al. 2005) Mamu-KIR3DL02 Mamu-KIR3DL02*002 KIR3DL-like_3 AY505478 (Andersen et al. 2004) Mamu-KIR3DL02 Mamu-KIR3DL02*003 KIR3DL21*001-BNB EU419050 (Moreland et al. 2011) Mamu-KIR3DL02 Mamu-KIR3DL02*004:01 KIR3DL21*003-BNB EU419052 (Moreland et al. 2011) Mamu-KIR3DL02 Mamu-KIR3DL02*004:02 KIR3DL21*005-BNB EU419053 (Moreland et al. 2011) Mamu-KIR3DL02 Mamu-KIR3DL02*005 KIR3DL21*006-BNB EU419054 (Moreland et al. 2011) Mamu-KIR3DL02 Mamu-KIR3DL02*006 KIR3DL21-like1 EU688989 (Moreland et al. 2011) Mamu-KIR3DL02 Mamu-KIR3DL02*007 None GU112277 (Blokhuis et al. 2010) Mamu-KIR3DL02 Mamu-KIR3DL02*008 None GU112281 (Blokhuis et al. 2010) Mamu-KIR3DLW03 Mamu-KIR3DLW03*001 KIR3DL21*002-BNB EU419051 (Moreland et al. 2011) Mamu-KIR3DLW03 Mamu-KIR3DLW03*002 KIR3DL21*007-BNB EU419055 (Moreland et al. 2011) Mamu-KIR3DLW03 Mamu-KIR3DLW03*003 KIR3DL-like1-BNB EU419031 (Moreland et al. 2011) Mamu-KIR3DLW03 Mamu-KIR3DLW03*004 KIR3DL-4 FN424253 (Kruse et al. 2010) Mamu-KIR3DLW03 Mamu-KIR3DLW03*005 KIR3DL-5 FN424256 (Kruse et al. 2010) Mamu-KIR3DL04 Mamu-KIR3DL04*001:01 KIR3DL11*002-BNB EU419040 (Moreland et al. 2011) Mamu-KIR3DL04 Mamu-KIR3DL04*001:02 None GU112311 (Blokhuis et al. 2010) Mamu-KIR3DL04 Mamu-KIR3DL04*001:03 None GU112319 (Blokhuis et al. 2010) Mamu-KIR3DL04 Mamu-KIR3DL04*002 KIR3DL11*003-BNB EU419042 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*001 KIR3DL16*001-BNB EU419045 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*002 KIR3DL7*004-BNB EU419061 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*003 KIR3DL7*005-BNB EU419062 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*004 KIR3DL7*009-BNB EU419066 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*005 KIR3DL7*013-BNB EU419069 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*006:01 KIR3DL7-like2 EU688991 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*006:02 None GU112293 (Blokhuis et al. 2010) Mamu-KIR3DL05 Mamu-KIR3DL05*007 KIR3DL-3 FN424252 (Kruse et al. 2010) Mamu-KIR3DL05 Mamu-KIR3DL05*008 3DL7b-3DL40 GU112291, GU014295 (Blokhuis et al. 2010) (Colantonio et al. 2011) 576 Immunogenetics (2018) 70:571–583 Table 4 (continued) Gene Allele designation Previous designations Accession number Reference Mamu-KIR3DL05 Mamu-KIR3DL05*009 None GU112310 (Blokhuis et al. 2010) Mamu-KIR3DL05 Mamu-KIR3DL05*010 KIR3DL allele 13 FJ562120 (Bostik et al. 2009) Mamu-KIR3DL05 Mamu-KIR3DL05*011 KIR3DL allele 14 FJ562121 (Bostik et al. 2009) Mamu-KIR3DL06 Mamu-KIR3DL06*001 KIR3DL6 AF334621 (Hershberger et al. 2001) Mamu-KIR3DL06 Mamu-KIR3DL06*002 KIR3DL6*001-BNB EU419056 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*001 KIR3DL7 AF334622 (Hershberger et al. 2001) Mamu-KIR3DL07 Mamu-KIR3DL07*002 KIR3DL18 AF361086 (Grendell et al. 2001) Mamu-KIR3DL07 Mamu-KIR3DL07*003 KIR3DL7*001-BNB EU419057 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*004 KIR3DL7*003-BNB EU419060 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*005 KIR3DL7*006-BNB EU419063 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*006 KIR3DL7*007-BNB EU419064 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*007 KIR3DL7*008-BNB EU419065 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*008 KIR3DL7*012-BNB EU419068 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*009:01 KIR3DL7-like1, 2DL420 EU688990, GU299489 (Colantonio et al. 2011; Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*009:02 None GU112282 (Blokhuis et al. 2010) Mamu-KIR3DL07 Mamu-KIR3DL07*010 KIR3DL7-like3 EU688992 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*011 KIR3DL allele 10 FJ562117 (Bostik et al. 2009) Mamu-KIR3DL07 Mamu-KIR3DL07*012 KIR3DL allele 11 FJ562118 (Bostik et al. 2009) Mamu-KIR3DL08 Mamu-KIR3DL08*001:01 KIR3DL8 AY728189 (Sambrook et al. 2005) Mamu-KIR3DL08 Mamu-KIR3DL08*001:02 KIR3DL8*002-BNB EU419071 (Moreland et al. 2011) Mamu-KIR3DL08 Mamu-KIR3DL08*002 KIR3DL17 AF361084, GU112306 (Blokhuis et al. 2010; Grendell et al. 2001) Mamu-KIR3DL08 Mamu-KIR3DL08*003 KIR3DL17 AF361085 (Grendell et al. 2001) Mamu-KIR3DL08 Mamu-KIR3DL08*004 KIR3DL-like_2 AY505477 (Andersen et al. 2004) Mamu-KIR3DL08 Mamu-KIR3DL08*005 KIRDL8 AY728189 (Sambrook et al. 2005) R3DL08 Mamu-KIR3DL08*006 KIR3DL8*001-BNB EU419070 (Moreland et al. 2011) Mamu-KI Mamu-KIR3DL08 Mamu-KIR3DL08*007 None GU112268 (Blokhuis et al. 2010) Mamu-KIR3DL08 Mamu-KIR3DL08*008 None GU112285 (Blokhuis et al. 2010) Mamu-KIR3DL08 Mamu-KIR3DL08*009 None GU112290 (Blokhuis et al. 2010) Mamu-KIR3DL08 Mamu-KIR3DL08*010 None GU112330 (Blokhuis et al. 2010) Mamu-KIR3DL08 Mamu-KIR3DL08*011 KIR3DL allele 8 FJ562115 (Bostik et al. 2009) Mamu-KIR3DL10 Mamu-KIR3DL10*001 KIR3DL10 AY728183 (Sambrook et al. 2005) Mamu-KIR3DL10 Mamu-KIR3DL10*002:01 KIR3DL9, KIR3DL allele 5 AF334624, GU112259, (Hershberger et al. FJ562112 2001)(Blokhuis et al. 2010; Bostik et al. 2009) Mamu-KIR3DL10 Mamu-KIR3DL10*002:02 3DL3NK GU299486 (Colantonio et al. 2011) Mamu-KIR3DL10 Mamu-KIR3DL10*003 KIR3DL10*001-BNB EU419038 (Moreland et al. 2011) Mamu-KIR3DL10 Mamu-KIR3DL10*004 KIR3DL10*002-BNB EU419039 (Moreland et al. 2011) Mamu-KIR3DL10 Mamu-KIR3DL10*005:01 3DL10-2DL501 GU014294 (Colantonio et al. 2011) Mamu-KIR3DL10 Mamu-KIR3DL10*005:02 None GU112295 (Blokhuis et al. 2010) Mamu-KIR3DL10 Mamu-KIR3DL10*006 KIR3DL allele 6 FJ562113 (Bostik et al. 2009) Mamu-KIR3DL11 Mamu-KIR3DL11*001 KIR3DL11 AF334626, GU112271 (Blokhuis et al. 2010; Hershberger et al. 2001) Mamu-KIR3DL11 Mamu-KIR3DL11*002 KIR3DL-1 FN424250 (Kruse et al. 2010) Mamu-KIR3DL11 Mamu-KIR3DL11*003 KIR3DL-6 FN424259 (Kruse et al. 2010) Mamu-KIR3DL11 Mamu-KIR3DL11*004 KIR3DL-7 FN424261 (Kruse et al. 2010) Mamu-KIR3DL11 Mamu-KIR3DL11*005 None GU112276 (Blokhuis et al. 2010) Mamu-KIR3DL11 Mamu-KIR3DL11*006 None GU112296 (Blokhuis et al. 2010) Mamu-KIR3DL11 Mamu-KIR3DL11*007 KIR3DL allele 9 FJ562116 (Bostik et al. 2009) Immunogenetics (2018) 70:571–583 577 Table 4 (continued) Gene Allele designation Previous designations Accession number Reference Mamu-KIR3DL20 Mamu-KIR3DL20*001 KIR3DL20*001-BNB EU419047 (Moreland et al. 2011) Mamu-KIR3DL20 Mamu-KIR3DL20*002 KIR3DL20 AY728184, GU112327 (Blokhuis et al. 2010; Sambrook et al. 2005) Mamu-KIR3DL20 Mamu-KIR3DL20*003 KIR3DL20_variant_2 AY728186 (Sambrook et al. 2005) Mamu-KIR3DL20 Mamu-KIR3DL20*004 KIR3DL20*003-BNB EU419048 (Moreland et al. 2011) Mamu-KIR3DL20 Mamu-KIR3DL20*005 KIR3DL20*004-BNB EU419049 (Moreland et al. 2011) Mamu-KIR3DL20 Mamu-KIR3DL20*006 None GU112255 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*007 None GU112256 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*008 None GU112264 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*009 None GU112270 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*010 None GU112275 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*011 None GU112289 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*012 None GU112299 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*013 None GU112304, GU112317 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*014 None GU112308 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*015 None GU134802 (Blokhuis et al. 2010) Mamu-KIR3DS01 Mamu-KIR3DS01*001:01 KIR3DH5 AF361087 (Grendell et al. 2001) Mamu-KIR3DS01 Mamu-KIR3DS01*001:02 None GU112307 (Blokhuis et al. 2010) Mamu-KIR3DS01 Mamu-KIR3DS01*002 KIR3DH1 AY728190 (Sambrook et al. 2005) Mamu-KIR3DS01 Mamu-KIR3DS01*003 KIR3DH-7 GU564161 (Chaichompoo et al. 2010) Mamu-KIR3DS02 Mamu-KIR3DS02*001 KIR3DH2 AF334649 (Hershberger et al. 2001) Mamu-KIR3DS02 Mamu-KIR3DS02*002 KIR3DH-like_5 AY505483 (Andersen et al. 2004) Mamu-KIR3DS02 Mamu-KIR3DS02*003 KIR3DH-like_6 AY505484 (Andersen et al. 2004) Mamu-KIR3DS02 Mamu-KIR3DS02*004:01 KIR3DH2*001-BNB, KIR3DH14 EU419026, EU702460 (Blokhuis et al. 2009a; Moreland et al. 2011) Mamu-KIR3DS02 Mamu-KIR3DS02*004:02 KIR3DH13, 3DH42 EU702459, GU014296 (Blokhuis et al. 2009a) (Colantonio et al. 2011) mu-KIR3DS02 Mamu-KIR3DS02*004:03 KIR3DH12 EU702458 (Blokhuis et al. 2009a) Ma Mamu-KIR3DS02 Mamu-KIR3DS02*005 KIR3DH2*002-BNB EU419027 (Moreland et al. 2011) Mamu-KIR3DS02 Mamu-KIR3DS02*006 KIR3DH16 EU702462 (Blokhuis et al. 2009a) Mamu-KIR3DS02 Mamu-KIR3DS02*007 KIR3DH15 EU702461 (Blokhuis et al. 2009a) Mamu-KIR3DS02 Mamu-KIR3DS02*008 KIR3DH10 EU702456, GU112278 (Blokhuis et al. 2009a; Blokhuis et al. 2010) Mamu-KIR3DS02 Mamu-KIR3DS02*009 None GU112261, GU112315 (Blokhuis et al. 2010) Mamu-KIR3DS02 Mamu-KIR3DS02*010 None GU112297 (Blokhuis et al. 2010) Mamu-KIR3DS02 Mamu-KIR3DS02*011 None GU112323 (Blokhuis et al. 2010) Mamu-KIR3DS02 Mamu-KIR3DS02*012 3DH2*NEW1 JN613291 (Hellmann et al. 2011) Mamu-KIR3DS02 Mamu-KIR3DS02*013 3DH2*NEW1 JN613299 (Hellmann et al. 2011) Mamu-KIR3DS03 Mamu-KIR3DS03*001:01 KIR3DH3 AF334650, GU112312 (Hershberger et al. 2001) (Blokhuis et al. 2010) Mamu-KIR3DS03 Mamu-KIR3DS03*001:02 None GU112294 (Blokhuis et al. 2010) Mamu-KIR3DS03 Mamu-KIR3DS03*002 KIR3DH9 EU702455, GU112269 (Blokhuis et al. 2009a; Blokhuis et al. 2010) Mamu-KIR3DS03 Mamu-KIR3DS03*003 KIR3DH8 EU702454 (Blokhuis et al. 2009a) Mamu-KIR3DS04 Mamu-KIR3DS04*001 KIR3DH4 AF334651 (Hershberger et al. 2001) Mamu-KIR3DS04 Mamu-KIR3DS04*002 KIR3DH4*001-BNB EU419028 (Moreland et al. 2011) Mamu-KIR3DS04 Mamu-KIR3DS04*003 KIR3DH4*002-BNB, KIR3DH4 EU419029, JN613296 (Hellmann et al. 2011; Moreland et al. 2011) Mamu-KIR3DS04 Mamu-KIR3DS04*004 KIR3DH6 EU702452 (Blokhuis et al. 2009a) Mamu-KIR3DS04 Mamu-KIR3DS04*005 KIR3DH4 JN613300 (Hellmann et al. 2011) 578 Immunogenetics (2018) 70:571–583 Table 4 (continued) Gene Allele designation Previous designations Accession number Reference Mamu-KIR3DS04 Mamu-KIR3DS04*006 KIR3DH-1 GU564157 (Chaichompoo et al. 2010) Mamu-KIR3DS05 Mamu-KIR3DS05*001 KIR3DH1*001-BNB EU419024, EU419025, (Moreland et al. 2011) EU702468, AY505487, GU112262 Mamu-KIR3DS05 Mamu-KIR3DS05*002:01 KIR3DH1*002-BNB, KIR3DM1, EU419025, EU702468, (Andersen et al. 2004; KIR_Partial_Sequence_1 AY505487, GU112262 Blokhuis et al. 2009a; Blokhuis et al. 2010; Moreland et al. 2011) Mamu-KIR3DS05 Mamu-KIR3DS05*002:02 KIR3DM6 EU702473 (Blokhuis et al. 2009a) Mamu-KIR3DS05 Mamu-KIR3DS05*003 KIR3DM-1 FN424260 (Kruse et al. 2010) Mamu-KIR3DS06 Mamu-KIR3DS06*001 KIR3DH-like_7 AY505485 (Andersen et al. 2004) Mamu-KIR3DS06 Mamu-KIR3DS06*002:01 KIR3DH-like8 EU688985 (Moreland et al. 2011) Mamu-KIR3DS06 Mamu-KIR3DS06*002:02 None GU112298 (Blokhuis et al. 2010) Mamu-KIR3DS06 Mamu-KIR3DS06*003 KIR3DH18 EU702464 (Blokhuis et al. 2009a) Mamu-KIR3DS06 Mamu-KIR3DS06*004 KIR3DH-4 FN424257 (Kruse et al. 2010) Mamu-KIR3DS06 Mamu-KIR3DS06*005 None GU112260 (Blokhuis et al. 2010) Mamu-KIR3DS06 Mamu-KIR3DS06*006 None GU112314 (Blokhuis et al. 2010) Mamu-KIR3DSW07 Mamu-KIR3DSW07*001 KIR3DH7 EU702453, GU112272 (Blokhuis et al. 2009a; Blokhuis et al. 2010) Mamu-KIR3DSW07 Mamu-KIR3DSW07*002 KIR3DH-5 FN424258 (Kruse et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*001 KIR3DH-like_1 AY505479 (Andersen et al. 2004) Mamu-KIR3DSW08 Mamu-KIR3DSW08*002 KIR3DH-like_2 AY505480 (Andersen et al. 2004) Mamu-KIR3DSW08 Mamu-KIR3DSW08*003 KIR3DH-like_3 AY505481 (Andersen et al. 2004) Mamu-KIR3DSW08 Mamu-KIR3DSW08*004 KIR3DH-like_4 AY505482 (Andersen et al. 2004) Mamu-KIR3DSW08 Mamu-KIR3DSW08*005 KIR3DH21 EU702467 (Blokhuis et al. 2009a) Mamu-KIR3DSW08 Mamu-KIR3DSW08*006 KIR3DH-2 FN424254 (Kruse et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*007 KIR3DH-3 FN424255 (Kruse et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*008 None GU112325 (Blokhuis et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*009 None GU112328 (Blokhuis et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*010 KIR3DSW08 JN613297 (Hellmann et al. 2011) Mamu-KIR3DSW08 Mamu-KIR3DSW08*011 KIR3DH-4 GU564158 (Chaichompoo et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*012 KIR3DH-5 GU564159 (Chaichompoo et al. 2010) Mamu-KIR3DSW09 Mamu-KIR3DSW09*001 KIR3DH5*001-BNB EU419030 (Moreland et al. 2011) Mamu-KIR3DSW09 Mamu-KIR3DSW09*002 KIR3DH5-like1 EU688986 (Moreland et al. 2011) Mamu-KIR3DSW09 Mamu-KIR3DSW09*003 None GU112301 (Blokhuis et al. 2010) Mamu-KIR3DSW09 Mamu-KIR3DSW09*004 KIR3DH20 EU702466, GU112273 (Blokhuis et al. 2009a), (Blokhuis et al. 2010) Mamu-KIR3DSW09 Mamu-KIR3DSW09*005 mmKIR3DH-1 FN424249 (Kruse et al. 2010) Mamu-KIR3DSW09 Mamu-KIR3DSW09*006 KIR3DH-8 GU564162 (Chaichompoo et al. 2010) Mamu-KIR3DLX1 Mamu-KIR3DLX1*001 KIR3DL0 DQ157756 (Sambrook et al. 2006) the sequence originally named Mamu-KIR3DL5 (Hershberger primate lineage 1 KIR, referred to as 2DL4 and has been et al. 2001) is a recombinant of Mamu-KIR3DL01 and Mamu- named Mamu-KIR2DL04. A single lineage III KIR is also KIR3DL07. As such, it has been renamed as an allele of present on some Mamu-KIR haplotypes and in all cases Mamu-KIR3DL01, Mamu-KIR3DL01*005. This principal appears to be expressed as a one Ig domain KIR. It has been has also been applied to recombinant alleles in other species. named Mamu-KIR1D. Finally, there is a lineage V KIR gene Along with the lineage II KIR genes, rhesus macaques that is expressed as either a two Ig or three Ig domain KIR. have KIR genes for lineage I, III, and V KIR. The lineage I The published genomic sequence shows the gene to contain KIR gene in rhesus macaques is orthologous to other three Ig domain encoding exons; however, due to splicing Immunogenetics (2018) 70:571–583 579 Table 5 Allele designations and their previous names Gene Allele designation Previous designations Accession number Reference Patr-KIR2DL4 Patr-KIR2DL4*001 None HM068617 (Abi-Rached et al. 2010) Patr-KIR2DL4 Patr-KIR2DL4*002 None AC155174, AF258804 (Khakoo et al. 2000) Patr-KIR2DL4 Patr-KIR2DL4*003 None BX842589 (Sambrook et al. 2005) Patr-KIR2DL5 Patr-KIR2DL5*001 None HM068617 (Abi-Rached et al. 2010) Patr-KIR2DL5 Patr-KIR2DL5*002 None AF274005 (Rajalingam et al. 2001) Patr-KIR2DL5 Patr-KIR2DL5*003 None AC155174 Patr-KIR2DL5 Patr-KIR2DL5*004 None BX842589 (Sambrook et al. 2005) Patr-KIR2DL5 Patr-KIR2DL5*005 None AF258805 (Khakoo et al. 2000) Patr-KIR2DL6 Patr-KIR2DL6*001 None BX842589, AM292662 (Sambrook et al. 2005) Patr-KIR2DL6 Patr-KIR2DL6*002 None AF258806 Patr-KIR2DL6 Patr-KIR2DL6*003 None AM292661 Patr-KIR2DL7 Patr-KIR2DL7*001 None HM068617 (Abi-Rached et al. 2010) Patr-KIR2DL8 Patr-KIR2DL8*001 None HM068617 (Abi-Rached et al. 2010) Patr-KIR2DL8 Patr-KIR2DL8*002 None AC155174, AM279149 Biassoni, unpublished Patr-KIR2DL8 Patr-KIR2DL8*003 None BX842589 (Sambrook et al. 2005) Patr-KIR2DL9 Patr-KIR2DL9*001 None AC155174 Patr-KIR2DL9 Patr-KIR2DL9*002 None AM292657 Biassoni, unpublished Patr-KIR2DL9 Patr-KIR2DL9*003 None AM400233 Biassoni, unpublished Patr-KIR2DS4 Patr-KIR2DS4*001 None HM068617 Patr-KIR2DS4 Patr-KIR2DS4*002 None AF258807 Patr-KIR3DL1 Patr-KIR3DL1*001:01 None AC155174 Patr-KIR3DL1 Patr-KIR3DL1*001:02 None AF266729 (Rajalingam et al. 2001) Patr-KIR3DL1 Patr-KIR3DL1*002 None BX842589, AF258798 (Sambrook et al. 2005) Patr-KIR3DL1 Patr-KIR3DL1*003 None AF266730 (Rajalingam et al. 2001) Patr-KIR3DL1 Patr-KIR3DL1*004 None AF258799 Patr-KIR3DL1 Patr-KIR3DL1*005 None HM068617 Patr-KIR3DL3 Patr-KIR3DL3*001 None HM068617 Patr-KIR3DL3 Patr-KIR3DL3*002 None BX842589 Patr-KIR3DL3 Patr-KIR3DL3*003 None AC155174 Patr-KIR3DL3 Patr-KIR3DL3*004 None AY327500 Patr-KIR3DL4 Patr-KIR3DL4*001:01 None AM400232 Biassoni, unpublished Patr-KIR3DL4 Patr-KIR3DL4*001:02 None AF258800 (Khakoo et al. 2000) Patr-KIR3DL4 Patr-KIR3DL4*002 None HM068617 (Abi-Rached et al. 2010) Patr-KIR3DL5 Patr-KIR3DL5*001 None AM400235 Biassoni, unpublished Patr-KIR3DL5 Patr-KIR3DL5*003:01 None AF258801 (Khakoo et al. 2000) Patr-KIR3DL5 Patr-KIR3DL5*004 None AC155174, AM292659 Biassoni, unpublished Patr-KIR3DS2 Patr-KIR3DS2*001 None AC155174 Patr-KIR3DS2 Patr-KIR3DS2*002 None AF258803 Patr-KIR3DS6 Patr-KIR3DS6*001 None AM396937 Biassoni, unpublished out of exon 4, also two Ig domain KIR variants are of some of these sequences as Mamu-KIR2DL5.The pres- expressed. The majority of the rhesus macaque gene se- ence of the intact gene as evidenced by the published geno- quence appears orthologous to hominoid KIR3DL3 se- mic sequence, as well as the existence of full-length [three quences, the exception being exon 3 [encoding the D0 do- Ig domain containing] sequences has led us to propose nam- main] which appears more like the hominoid KIR2DL5 se- ing this gene as Mamu-KIR3DL20. This distinguishes this quences. This sequence relationship coupled with the pres- gene from the remaining Mamu-KIR3DL as well as ence of splice variants that lacked exon 4 led to the naming retaining the name of one of the first mRNA sequences that 580 Immunogenetics (2018) 70:571–583 Table 6 Allele designations and their previous names Gene Allele designation Previous designations Accession number Reference Poab-KIR2DL10 Poab-KIR2DL10*001 2DLA AF470358 (Guethlein et al. 2002) Poab-KIR2DL11 Poab-KIR2DL11*001 2DLB EF014479 (Guethlein et al. 2007b) Poab-KIR2DL12 Poab-KIR2DL12*001 2DLC AC200148 Poab-KIR2DL5 Poab-KIR2DL5*001 2DL5 AC200148 Poab-KIR2DS10 Poab-KIR2DS10*001 None AF470364 (Guethlein et al. 2002) Poab-KIR2DS13 Poab-KIR2DS13*001 2DSC1/2DSB AF470362 (Guethlein et al. 2002) Poab-KIR2DS14 Poab-KIR2DS14*001 2DSB/2DSD2 AF470361 (Guethlein et al. 2002) Poab-KIR2DS14 Poab-KIR2DS14*002 2DSA/2DSD1 AF470360 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*001:01 3DLH AF470373 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*001:02 None AC200148 Poab-KIR3DL1 Poab-KIR3DL1*002 3DLC AF470367 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*003 None AF470372 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*004:01 3DLD2 AF470369 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*004:02 3DLD1 EF014479 (Guethlein et al. 2007b) Poab-KIR3DL1 Poab-KIR3DL1*005 3DLA AF470365 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*006 3DLI AF470374 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*007 3DLB AF470366 (Guethlein et al. 2002) Poab-KIR3DL3 Poab-KIR3DL3*001 3DL3 AC200148 Poab-KIR3DS1 Poab-KIR3DS1*001 3DS1 AF470375 (Guethlein et al. 2002) Poab-KIRDP Poab-KIRDP*001 DP AC200148 Popy-KIR2DS10 Popy-KIR2DS10*001 2DSD/2DSA AF470364 (Guethlein et al. 2002) Popy-KIR2DS13 Popy-KIR2DS13*001 2DSC2/2DSB AF470363 (Guethlein et al. 2002) Popy-KIR3DL1 Popy-KIR3DL1*001 3DLF AF470372 (Guethlein et al. 2002) Popy-KIR3DL1 Popy-KIR3DL1*002:01 3DLE2 AF470371 (Guethlein et al. 2002) Popy-KIR3DL1 Popy-KIR3DL1*002:02 3DLE1 AF470370 (Guethlein et al. 2002) included all three Ig domain encoding exons, see Table 1 for showed that Pt-KIR3DL3 and KIR3DL1/2 were never present further details. A full list of Mamu-KIR sequences is de- on the same haplotype, Pt-KIR3DL3 was given a different scribedinTable 4. name because it has a distinctive sequence. We are renaming The identification of sequences in other Macaque species the Pt-KIRDl1/2 and Pt-KIR3DL3 as allelic variants of Patr- will follow the same rules, and use the species prefix (Mafa- KIR3DL1, the new name for the framework gene at the KIR, Mane-KIR), and that genes would be named to match telomeric end of the chimpanzee KIR locus. This will allow the closest rhesus gene. the Patr-KIR3DL3 name to be given to the gene previously known as Patr-KIRC1, and which is orthologous to human KIR3DL3, the framework gene at the centromeric end of the Naming chimpanzee KIR genes KIR locus. See Table 2 for further details. A full list of Patr- KIR sequences is described in Table 5. Three studies (Abi-Rached et al. 2010;Khakoo et al. 2000; Sambrook et al. 2005) have described complete sequences of three chimpanzee haplotypes. In addition, the analysis of chim- Naming orangutan KIR genes panzee KIR genotypes has inferred the organization of genes infers the existence of another 17 chimpanzee KIR haplotypes. In the initial description of orangutan KIR cDNA (Guethlein et These analyses have defined 13 different Patr-KIR genes. al. 2002), the sequences were given letter designations be- In all chimpanzee KIR haplotypes, the framework gene at cause their relationships, either alleles or genes, were uncer- the telomeric end is a lineage II KIR gene. Formerly, two tain. Subsequent studies (Guethlein et al. 2007a;Guethlein et variants, now known to occupy this position, were named al. 2017; Locke et al. 2011; Mager et al. 2001)have provided Pt-KIR3DL1/2 and Pt-KIR3DL3. The name Pt-KIR3DL1/2 complete sequences of three orangutan KIR haplotypes, as was given to reflect its close relationship to both human well as genotyping data that has allowed the structures of KIR3DL1 and KIR3DL2. Although segregation analysis two additional KIR haplotypes to be inferred. These genomic Immunogenetics (2018) 70:571–583 581 Table 7 Allele designations and their previous names Gene Allele designation Previous Accession number Breed Reference designations Bota-KIR2DL1 Bota-KIR2DL1*001 KIR2DL1 AY075102,AF490399 UnknownHolstein (McQueen et al. 2002; Storset et al. 2003; Zimin et al. 2009) Bota-KIR2DL1 Bota-KIR2DL1*002 None JX848327 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR2DS1 Bota-KIR2DS1*001N KIR2DS1 JX848328 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR2DS2 Bota-KIR2DS2*001N None JX848329 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR2DS3 Bota-KIR2DS3*001N None JX848330 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR2DXS1 Bota-KIR2DXS1*001 None AF490400 Holstein (Storset et al. 2003) Bota-KIR2DXP1 Bota-KIR2DXP1*001 None JX848331 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR2DXP2 Bota-KIR2DXP2*001 None JX848332 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL1 Bota-KIR3DXL1*001 KIR3DL1 AF490402 Holstein (Storset et al. 2003; Zimin et al. 2009) Bota-KIR3DXL1 Bota-KIR3DXL1*002 None JX848333 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL2 Bota-KIR3DXL2*001 None JX848334 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL3 Bota-KIR3DXL3*001 None JX848335 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL4 Bota-KIR3DXL4*001 KIR3DL2–001 EF197118 Holstein-Freisian (Dobromylskyj and Ellis 2007; Zimin et al. 2009) Bota-KIR3DXL4 Bota-KIR3DXL4*002 None JX848336 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL5 Bota-KIR3DXL5*001 None JX848337 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL6 Bota-KIR3DXL6*001N KIR3DL1P AY075103JX848338 UnknownHolstein-Freisian (McQueen et al. 2002) (Sanderson et al. 2014) Bota-KIR3DXL6 Bota-KIR3DXL6*002 KIR3DL3 EF197119 Holstein-Freisian (Dobromylskyj and Ellis 2007; Zimin et al. 2009) Bota-KIR3DXL7 Bota-KIR3DXL7*001 None JX848339 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXS1 Bota-KIR3DXS1*001 KIR3DS1 AF490401 Holstein (Storset et al. 2003; Zimin et al. 2009) Bota-KIR3DXS1 Bota-KIR3DXS1*002 KIR3DS1–002 EF197120 Holstein-Freisian (Dobromylskyj and Ellis 2007) Bota-KIR3DXS1 Bota-KIR3DXS1*003 None JX848340 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXS2 Bota-KIR3DXS2*001N None JX848341 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXS3 Bota-KIR3DXS3*001N None JX848342 Holstein-Freisian (Sanderson et al. 2014) data, in combination with the cDNA sequences, defined 11 Ellis 2007; Guethlein et al. 2007a; Hammond et al. 2016; KIR genes and 1 KIR pseudogene in the orangutan. At first, all Mager et al. 2001; Sanderson et al. 2014). This presents the orangutan KIR were named as BPopy^ (Guethlein et al. opportunity to adopt an accurate and logical nomenclature 2007b). The orangutan KIR is now divided into two series system. Cattle KIR cDNA sequences were previously named corresponding to the two species of orangutan: Popy for using the established convention of Ig domain number and tail Pongo pygmaeus and Poab for Pongo abelii depending on length. However, these alleles were annotated prior to the species of origin. Some KIR alleles are present in both orang- discovery of a second deeply divergent KIR lineage, the utan species. These alleles shared have been given a different KIR3DX lineage (Guethlein et al. 2007a). The majority of name in each species (Guethlein et al. 2017; Guethlein et al. the expanded cattle KIR belong to this second lineage. In 2015), see Table 3: for further details. A full list of Popy-KIR developing a nomenclature system for the cattle KIR,we have and Poab-KIR sequences is given in Table 6. incorporate their lineage ancestry within the name. Cattle KIR have been prefixed with a four-letter species designation BBota^ (Bos taurus) in line with non-human primates. Naming cattle KIR genes Where possible previously named Bota-KIR has retained the same name with only the addition of an BX^ after the domain Assembly of the first cattle KIR haplotype allowed previously number if from the KIR3DX lineage. There are three excep- known cDNA sequences to be assigned to particular genes tions; Bota-KIR3DL1P and Bota-KIR3DL3, which are allelic, and allelic relationships to be defined (Dobromylskyj and 582 Immunogenetics (2018) 70:571–583 Fig. 1 Non-human KIR nomenclature. Details the syntax and structure of a non-human KIR allele designation and Bota-KIR3DL2. These previously described cDNA se- References quences are all members of the KIR3DX lineage. Based on their position in the cattle haplotype and their relationships Abi-Rached L, Moesta AK, Rajalingam R, Guethlein LA, Parham P (2010) Human-specific evolution and adaptation led to major qual- to other genes, Bota-KIR3DL1P was renamed Bota- itative differences in the variable receptors of human and chimpan- KIR3DXL6*001N, Bota-KIR3DL3 was renamed Bota- zee natural killer cells. PLoS Genet 6:e1001192 KIR3DXL6*002,and Bota-KIR3DL2 was renamed Bota- Andersen H, Rossio JL, Coalter V, Poore B, Martin MP, Carrington M, KIR3DXL4. We haveidentified16 cattle KIR genes. The pro- Lifson JD (2004) Characterization of rhesus macaque natural killer activity against a rhesus-derived target cell line at the single-cell posed nomenclature for cattle KIR is given in Table 7. level. Cell Immunol 231:85–95 Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Future guidelines Ostell J, Sayers EW (2017) GenBank. Nucleic Acids Res 45: D37–D42 The sequences described in this report will be included in the Blokhuis JH, Doxiadis GG, Bontrop RE (2009a) A splice site mutation converts an inhibitory killer cell Ig-like receptor into an activating Immuno Polymorphism Database (IPD) (Robinson et al. 2013). one. Mol Immunol 46:640–648 They will be maintained as a component of the IPD and be Blokhuis JH, van der Wiel MK, Doxiadis GG, Bontrop RE (2009b) accessible at https://www.ebi.ac.uk/ipd/nhkir/. New sequences Evidence for balancing selection acting on KIR2DL4 genotypes in for any of the above species can be submitted using the current rhesus macaques of Indian origin. Immunogenetics 61:503–512 submission tool. As with the other databases, there are Blokhuis JH, van der Wiel MK, Doxiadis GG, Bontrop RE (2010) The mosaic of KIR haplotypes in rhesus macaques. Immunogenetics 62: requirements that should be met before formal names can be 295–306 given and the submitted KIR are included in the database. First, Bostik P, Kobkitjaroen J, Tang W, Villinger F, Pereira LE, Little DM, submission of full-length sequences is encouraged and for some Stephenson ST, Bouzyk M, Ansari AA (2009) Decreased NK cell species like rhesus macaque is already mandatory. Second, nov- frequency and function is associated with increased risk of KIR3DL allele polymorphism in simian immunodeficiency virus-infected el sequences must be confirmed, either through their replication rhesus macaques with high viral loads. J Immunol 182:3638–3649 in multiple individuals or at a minimum by coming from mul- Chaichompoo P, Bostik P, Stephenson S, Udompunturuk S, Kobkitjaroen tiple independent PCR/cloning experiments. Full guidelines for J, Pattanapanyasat K, Ansari AA (2010) Multiple KIR gene poly- submission of non-human KIR sequences to IPD can be found morphisms are associated with plasma viral loads in SIV-infected at https://www.ebi.ac.uk/ipd/nhkir/submission/help. rhesus macaques. Cell Immunol 263:176–187 Chojnacki S, Cowley A, Lee J, Foix A, Lopez R (2017) Programmatic As KIR sequence data from other species reaches the level access to bioinformatics tools from EMBL-EBI update: 2017. of the species included in this report, those species can be Nucleic Acids Res 45:W550–W553 included in the database. The inclusion of a species will be Colantonio AD, Bimber BN, Neidermyer WJ Jr, Reeves RK, Alter G, at the discretion of the Nomenclature Committee and IPD and Altfeld M, Johnson RP, Carrington M, O'Connor DH, Evans DT will be based on the number of sequences available as well as (2011) KIR polymorphisms modulate peptide-dependent binding to an MHC class I ligand with a Bw6 motif. PLoS Pathog 7: evidence of identified genes and haplotype structure. e1001316 de Groot NG, Otting N, Robinson J, Blancher A, Lafont BA, Marsh Funding JAH and NDS were supported by the United Kingdom SGE, O'Connor DH, Shiina T, Walter L, Watkins DI, Bontrop Biotechnology and Biological Sciences Research Council (BBSRC) RE (2012) Nomenclature report on the major histocompatibility through projects BBS/E/I/00001410 and BBS/E/I/00001710. complex genes and alleles of great ape, old and new world monkey species. Immunogenetics 64:615–631 Open Access This article is distributed under the terms of the Creative Dobromylskyj M, Ellis S (2007) Complexity in cattle KIR genes: tran- Commons Attribution 4.0 International License (http:// scription and genome analysis. 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A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Genome Biol 10:R42 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Immunogenetics Springer Journals
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Springer Berlin Heidelberg
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Copyright © 2018 by The Author(s)
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Biomedicine; Immunology; Human Genetics; Gene Function; Cell Biology; Allergology
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0093-7711
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10.1007/s00251-018-1064-4
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Abstract

The increasing number of Killer Immunoglobulin-like Receptor (KIR) sequences available for non-human primate species and cattle has prompted development of a centralized database, guidelines for a standardized nomenclature, and minimum require- ments for database submission. The guidelines and nomenclature are based on those used for human KIR and incorporate modifications made for inclusion of non-human species in the companion IPD-NHKIR database. Included in this first release are the rhesus macaque (Macaca mulatta), chimpanzee (Pan troglodytes), orangutan (Pongo abelii and Pongo pygmaeus), and cattle (Bos taurus). . . . . . . Keywords KIR Nomenclature Variant Allele Gene Database Sequence Introduction made it difficult to assign orthologues and have led to a num- ber of different nomenclature systems being used to name The KIR locus has been studied in a number of non-human genes and alleles. This report describes a common framework species primates and is characterized by high levels of allelic and guidelines for KIR nomenclature in non-human species. polymorphism, haplotypic polymorphism in the number of These have been developed by taking advantage of lessons genes, and extensive duplication and recombination learned in the development of a nomenclature system for the (Hammond et al. 2016; Parham 2004). These factors have human KIR (Marsh et al. 2003). General naming guidelines * Steven G. E. Marsh steven.marsh@ucl.ac.uk To provide consistency with the IPD-MHC Database (Maccari et al. 2017), the non-human KIR nomenclature Anthony Nolan Research Institute, London, UK adopts the same four-character prefix used for species desig- nation in the naming of MHC alleles (de Groot et al. 2012; UCL Cancer Institute, University College London, London, UK Ellis et al. 2006; Klein et al. 1990). Also, genes and alleles will Department of Structural Biology and Department of Microbiology be named based on the conventions that have been adopted for & Immunology, School of Medicine, Stanford University, Stanford, CA, USA the human KIR system (Marsh et al. 2003) that are based on the structures of the molecules they encode. The first digit The Pirbright Institute, Woking, UK following the KIR acronym corresponds to the number of Biomedical Primate Research Centre, Rijswijk, Netherlands Ig-like domains in the polypeptide and the BD^ denotes Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA BDomain.^ The D is followed by either an BL^ indicating a Oregon National Primate Research Centre, Oregon Health and BLong^ cytoplasmic tail, an BS^ indicating a BShort^ cytoplas- Science University, OR Beaverton, USA mic tail or a BP^ for pseudogenes. In addition, the inclusion of Nuffield Department of Clinical Medicine, University of Oxford, a BW^ indicates BWorkshop^ following the BL,^ BS,^ or BP^ to Oxford, UK indicate any sequence that by phylogenetic analysis is suffi- Aix-Marseille II University, Marseille, France ciently divergent to be considered a Bnew^ gene, but lack German Primate Centre, Gottingen, Germany either genomic sequencing or family studies to demonstrate 572 Immunogenetics (2018) 70:571–583 that it does define a new gene and not a divergent lineage a identity is known of the animal providing the sequenced known gene. Tables 1, 2,and 3 list the current gene designa- DNA, that information is included in the database, as well as tions and their previous names. Symbols for genes are itali- information regarding the origin of the animal. Tables 4, 5, 6, cized (e.g., Mamu-KIR3DL01), whereas symbols for proteins and 7 provide a complete list of genes and alleles currently in are not italicized (e.g., Mamu-KIR3DL01). Alleles follow the the nomenclature, as well as the original name(s), accession same conventions as gene names. number, and reference to the original report of the sequence. Reflecting species-specific differences, there have been Each KIR allele name includes a unique number corre- further additions/modifications to the general nomenclature sponding to up to three sets of digits separated by colons. for rhesus macaque and cattle. As with the human KIR no- All alleles are given a three-digit name, which corresponds menclature, alleles in each series have been named in order of to the first set of digits; longer names are assigned only their deposition into a generalist sequence databank, when necessary. GenBank/EMBL-ENA/DDBJ (Benson et al. 2017; The digits placed before the first colon describe the alleles Chojnacki et al. 2017; Mashima et al. 2017). Where the that differ at non-synonymous substitutions (also called coding Table 1 Gene designations and Species KIR gene Previous KIR gene designation(s) their previous names designation(s) Rhesus Mamu-KIR1D KIR1D, Mamu-KIR1D macaque Mamu-KIR2DL04 2DL501NK, 2DL503NK, KIR2DL4, KIR2DL4.1, MmKIR2DL4 (Mamu) Mamu-KIR3DL01 2DL426NK, 3DL34, KIR3DL, KIR3DL-like_1, KIR3DL1, KIR3DL1-like1, KIR3DL12, KIR3DL13, KIR3DL14, KIR3DL15, KIR3DL19, KIR3DL1_variant_2, KIR3DL2, KIR3DL2-old, KIR3DL3, KIR3DL4, KIR3DL5 Mamu-KIR3DL02 KIR3DL-like_3, KIR3DL2, KIR3DL21, KIR3DL21-like1 Mamu-KIR3DL04 KIR3DL11 Mamu-KIR3DL05 3DL7b-3DL40, KIR3DL, KIR3DL-3, KIR3DL16, KIR3DL7, KIR3DL7-like2, KIR3DL07 Mamu-KIR3DL06 KIR3DL6 Mamu-KIR3DL07 2DL420, KIR3DL, KIR3DL18, KIR3DL7, KIR3DL7-like1, KIR3DL7-like3, KIR3DL03 Mamu-KIR3DL08 KIR3DL, KIR3DL-like_2, KIR3DL17, KIR3DL8, KIRDL8, Mamu-KIR3DL04, Mamu-KIR3DL4 Mamu-KIR3DL10 3DL10-2DL501, 3DL3NK, KIR3DL, KIR3DL10, KIR3DL9, Mamu-KIR3DL05 Mamu-KIR3DL11 KIR3DL, KIR3DL-1, KIR3DL-6, KIR3DL-7, KIR3DL11 Mamu-KIR3DL20 KIR3DL20, KIR3DL20_variant_2, KIR3DL06, KIR2DL5 Mamu-KIR3DLW03 KIR3DL-4, KIR3DL-5, KIR3DL-like1-BNB, KIR3DL21 Mamu-KIR3DLX1 KIR3DL0 Mamu-KIR3DS01 KIR3DH-7, KIR3DH1, KIR3DH5, Mamu-KIR3DS01-JHB-HEFGH, Mamu-KIR3DS02 3DH2, 3DH42, KIR3DH-like_5, KIR3DH-like_6, KIR3DH10, KIR3DH12, KIR3DH13, KIR3DH14, KIR3DH15, KIR3DH16, KIR3DH2 Mamu-KIR3DS03 KIR3DH3, KIR3DH8, KIR3DH9 Mamu-KIR3DS04 KIR3DH-1, KIR3DH4, KIR3DH6 Mamu-KIR3DS05 KIR3DH1, KIR3DM-1, KIR3DM1, KIR3DM6, KIR_Partial_ Sequence_1 Mamu-KIR3DS06 KIR3DH-4, KIR3DH-like8, KIR3DH-like_7, KIR3DH18, Mamu-KIR3DSW07 KIR3DH-5, KIR3DH7, Mamu-KIR3DS07-JHB-HO Mamu-KIR3DSW08 KIR3DH-2, KIR3DH-3, KIR3DH-4, KIR3DH-5, KIR3DH-like_1, KIR3DH-like_2, KIR3DH-like_3, KIR3DH-like_4, KIR3DH21, KIR3DSW08 Mamu-KIR3DSW09 KIR3DH-8, KIR3DH20, KIR3DH5, KIR3DH5-like1, mmKIR3DH-1 Immunogenetics (2018) 70:571–583 573 Table 2 Gene designations and their previous names second sets of digits. Alleles that only differ by sequence poly- morphisms in the introns, or in the 5′ or 3′ untranslated regions Species KIR gene Previous KIR gene designation(s) that flank the exons and introns, are distinguished by their third designation(s) sets of digits. Chimpanzee Patr-KIR2DL4 In addition to the unique allele number, optional suf- (Patr) Patr-KIR2DL5 fixescan be addedtoanallelename toindicatethe ex- Patr-KIR2DL6 Pt-NewII pression status of the gene and/or its encoded protein. Patr-KIR2DL7 Alleles known not to be expressed—so called BNull^ al- Patr-KIR2DL8 Pt-NewIII leles—have been given the suffix BN.^ Alleles that have Patr-KIR2DL9 been shown to be alternatively expressed may have the Patr-KIR3DL1 Pt-KIR3DL1/2, Pt-KIR3DL3, suffix BL,^ BS,^ BC,^ BA,^ or BQ.^ Pt-KIR3DL1, Pt-KIR3DL2 The suffix BL^ is used to indicate an allele that has been Patr-KIR3DL3 Patr-KIRC1, Pt-NewI shown to have BLow^ cell surface expression when compared Patr-KIR3DL4 to normal levels. The BS^ suffix is used to denote an allele Patr-KIR3DL5 specifying a protein which is expressed as a soluble, Patr-KIR3DS6 Pt-KIR3DL6 BSecreted^ molecule and is not present on the cell surface. The BC^ suffix is assigned to alleles producing proteins that are present in the BCytoplasm^ and not on the cell surface. An substitutions). Alleles that differ only by synonymous nucleo- BA^ suffix indicates an BAberrant^ expression, where there is tide substitutions (also called silent or non-coding substitutions) doubt as to whether a protein is actually expressed. A BQ^ but are within the coding sequence are distinguished by their suffix is used when the expression of an allele is BQuestionable,^ given that the mutation seen in the allele Table 3 Gene designations and their previous names has been shown to affect normal expression levels in other alleles and other KIR genes. Species KIR gene Previous KIR gene designation(s) As of May 2018, no alleles have been named with the BC,^ designation(s) BA,^ BQ,^ or BS^ suffixes. Orangutan Poab-KIR2DL10 Popy-KIR2DL10, 2DLA A schematic representation of the syntax for the non- (Poab) Poab-KIR2DL11 Popy-KIR2DL11, 2DLB human KIR allele designation is shown in Fig. 1. Poab-KIR2DL12 Popy-KIR2DL11, 2DLC Poab-KIR2DL5 Popy-KIR2DL5. 2DL5 Species-specific guidelines Poab-KIR2DS10 2DSD/2DSA Poab-KIR2DS13 Popy-KIR2DS13, 2DSC1/2DSB Naming rhesus macaque KIR genes Poab-KIR2DS14 Popy-KIR2DS14, 2DSB/2DSD2, 2DSA/2DSD1 The Mamu-KIR sequences fall into a number of distinct Poab-KIR3DL1 Popy-KIR3DL1, 3DLH, 3DLC, lineages based on phylogenetic analysis. Most sequences 3DLD2, 3DLD1, 3DLA, 3DLI, correspond to lineage II KIR and are further divided 3DLB into those encoding KIR that have long cytoplamic tails Poab-KIR3DL3 Popy-KIR3DL3, 3DL3 or short cytoplasmic tails. The genes have been num- Poab-KIR3DS1 Popy-KIR3DS1, 3DS1 bered sequentially and where possible the gene name Poab-KIRDP Popy-KIRDP, DP has the same the same number as the first reported Orangutan Popy-KIR2DL11 Popy-KIR2DLB allele for that gene. For example, the Mamu-KIR3DL1 (Popy) Popy-KIR2DL12 Popy-KIR2DLC gene (Hershberger et al. 2001)was renamed Mamu- Popy-KIR2DL5 KIR3DL01*001. Popy-KIR2DS10 Popy-KIR2DSD/2DSA The nomenclature uses a two-digit numbering of individ- Popy-KIR2DS13 Popy-KIR2DSC2/2DSB ual genes for the macaque sequences as seen with the nam- Popy-KIR2DS14 Popy-KIR2DSB/2DSD2, ing of Mamu-KIR3DL01*001. This renaming aims to avoid 2DSA/2DSD1 confusion with previous sequence names. Subsequent anal- Popy-KIR2DS15 ysis has shown that some of the proposed sequences of dif- Popy-KIR3DL1 Popy-KIR3DL1, 3DLF, 3DLE2, ferent genes are actually allelic variants of the same gene. 3DLE1 Rather than skipping numbers to avoid confusion, it was Popy-KIR3DL3 Popy-KIR3DL3, 3DL3 thought better to introduce the two-digit numbering system. Popy-KIR3DS1 Popy-KIR3DS1, 3DS1 Recombinant alleles are named according to the locus, Popy-KIRDP Popy-KIRDP, DP which provide the majority of the sequence. For example, 574 Immunogenetics (2018) 70:571–583 Table 4 Allele designations and their previous names Gene Allele designation Previous designations Accession number Reference Mamu-KIR1D Mamu-KIR1D*001 KIR1D AF334634 (Hershberger et al. 2001) Mamu-KIR1D Mamu-KIR1D*002 KIR1D,Mamu-KIR1D*00202-JHB-HA AY728181, GU112257, (Sambrook et al. 2005) GU112266, GU112332 (Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*001:01 KIR2DL4, KIR2DL4.1, EU702486, AF361088, (Blokhuis et al. 2009a; MmKIR2DL4*0010101-JHB AF334644, FJ824091, Blokhuis et al. 2009b; GU112331, GU112318, Blokhuis et al. 2010; GU112263, GU112303, Grendell et al. 2001; GU112287 Hershberger et al. 2001) Mamu-KIR2DL04 Mamu-KIR2DL04*001:02 2DL501NK GU299490 (Colantonio et al. 2011) Mamu-KIR2DL04 Mamu-KIR2DL04*002 MmKIR2DL4*0020101-JHB FJ824092, GU112279 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*003 KIR2DL4, AY505486, FJ824093, (Andersen et al. 2004; MmKIR2DL4*0040101-JHB GU112322, GU112284 Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*004 KIR2DL4 AY728182 (Sambrook et al. 2005) Mamu-KIR2DL04 Mamu-KIR2DL04*005 MmKIR2DL4*0050101-JHB FJ824094 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*006:01 MmKIR2DL4*0060101-JHB FJ824095 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*006:02 2DL503NK GU014298 (Colantonio et al. 2011) Mamu-KIR2DL04 Mamu-KIR2DL04*007 MmKIR2DL4*0070101-JHB FJ824096 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*008:01 MmKIR2DL4*0080101-JHB FJ824097 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*008:02 MmKIR2DL4*0080201-JHB FJ824098, GU112326 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*010 MmKIR2DL4*0100101-JHB FJ824100 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*011 MmKIR2DL4*0110101-JHB FJ824101 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*012 MmKIR2DL4*0120101-JHB FJ824102 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*013 MmKIR2DL4*0130101-JHB FJ824103 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*014:01 MmKIR2DL4*0140101-JHB FJ824104, GU112316 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*014:02 MmKIR2DL4*0140201-JHB FJ824105 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*015:01 MmKIR2DL4*0150101-JHB FJ824106, GU112313 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*015:02 MmKIR2DL4*0150201-JHB FJ824107, GU112280 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR2DL04 Mamu-KIR2DL04*016 MmKIR2DL4*0160101-JHB FJ824108 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*017 MmKIR2DL4*0170101-JHB FJ824109 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*018 MmKIR2DL4*0180101-JHB FJ824110 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*019 MmKIR2DL4*0190101-JHB FJ824111 (Blokhuis et al. 2009b) Mamu-KIR2DL04 Mamu-KIR2DL04*020 MmKIR2DL4*0200101-JHB FJ824112, GU112274 (Blokhuis et al. 2009b; Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*001 KIR3DL1, 3DL34 AF334616, GU299488 (Colantonio et al. 2011; Hershberger et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*002 KIR3DL2-old, 2DL426NK AF334617, GU299488 (Hershberger et al. 2001), (Colantonio et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*003 KIR3DL3 AF361083, GU112305 (Blokhuis et al. 2010; Grendell et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*004 KIR3DL4 AF334619 (Hershberger et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*005 KIR3DL5 AF334620 (Hershberger et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*006 KIR3DL12 AF361082 (Grendell et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*007N KIR3DL13 AF408151 (Grendell et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*008N KIR3DL14 AF408152 (Grendell et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*009N KIR3DL15 AF408153 (Grendell et al. 2001) Mamu-KIR3DL01 Mamu-KIR3DL01*010 KIR3DL19 AF408150 (Grendell et al. 2001) Immunogenetics (2018) 70:571–583 575 Table 4 (continued) Gene Allele designation Previous designations Accession number Reference Mamu-KIR3DL01 Mamu-KIR3DL01*011 KIR3DL1_variant_2 AY728187 (Sambrook et al. 2005) Mamu-KIR3DL01 Mamu-KIR3DL01*012 KIR3DL1*002-BNB, KIR3DL-like_1 EU419033, AY505476, (Andersen et al. 2004; GU112286 Blokhuis et al. 2010; Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*013 KIR3DL1*003-BNB EU419034 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*014 KIR3DL1*005-BNB EU419035 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*015 KIR3DL1*006-BNB EU419036 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*016 KIR3DL1*007-BNB EU419037, GU112258 (Blokhuis et al. 2010; Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*017 KIR3DL12*001-BNB EU419044 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*018 KIR3DL2*001-BNB EU419046 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*019:01 KIR3DL1*001-BNB EU419032, GU112300 (Blokhuis et al. 2010; Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*019:02 None GU112283 (Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*020 KIR3DL1-like1 EU688987 (Moreland et al. 2011) Mamu-KIR3DL01 Mamu-KIR3DL01*021 KIR3DL FJ562108 (Bostik et al. 2009) Mamu-KIR3DL01 Mamu-KIR3DL01*022 None GU112267 (Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*023 None GU112292 (Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*024 None GU112321 (Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*025 None GU112324 (Blokhuis et al. 2010) Mamu-KIR3DL01 Mamu-KIR3DL01*026 KIR3DL allele 2 FJ562109 (Bostik et al. 2009) Mamu-KIR3DL01 Mamu-KIR3DL01*027 KIR3DL allele 3 FJ562110 (Bostik et al. 2009) Mamu-KIR3DL02 Mamu-KIR3DL02*001 KIR3DL2 AY728188 (Sambrook et al. 2005) Mamu-KIR3DL02 Mamu-KIR3DL02*002 KIR3DL-like_3 AY505478 (Andersen et al. 2004) Mamu-KIR3DL02 Mamu-KIR3DL02*003 KIR3DL21*001-BNB EU419050 (Moreland et al. 2011) Mamu-KIR3DL02 Mamu-KIR3DL02*004:01 KIR3DL21*003-BNB EU419052 (Moreland et al. 2011) Mamu-KIR3DL02 Mamu-KIR3DL02*004:02 KIR3DL21*005-BNB EU419053 (Moreland et al. 2011) Mamu-KIR3DL02 Mamu-KIR3DL02*005 KIR3DL21*006-BNB EU419054 (Moreland et al. 2011) Mamu-KIR3DL02 Mamu-KIR3DL02*006 KIR3DL21-like1 EU688989 (Moreland et al. 2011) Mamu-KIR3DL02 Mamu-KIR3DL02*007 None GU112277 (Blokhuis et al. 2010) Mamu-KIR3DL02 Mamu-KIR3DL02*008 None GU112281 (Blokhuis et al. 2010) Mamu-KIR3DLW03 Mamu-KIR3DLW03*001 KIR3DL21*002-BNB EU419051 (Moreland et al. 2011) Mamu-KIR3DLW03 Mamu-KIR3DLW03*002 KIR3DL21*007-BNB EU419055 (Moreland et al. 2011) Mamu-KIR3DLW03 Mamu-KIR3DLW03*003 KIR3DL-like1-BNB EU419031 (Moreland et al. 2011) Mamu-KIR3DLW03 Mamu-KIR3DLW03*004 KIR3DL-4 FN424253 (Kruse et al. 2010) Mamu-KIR3DLW03 Mamu-KIR3DLW03*005 KIR3DL-5 FN424256 (Kruse et al. 2010) Mamu-KIR3DL04 Mamu-KIR3DL04*001:01 KIR3DL11*002-BNB EU419040 (Moreland et al. 2011) Mamu-KIR3DL04 Mamu-KIR3DL04*001:02 None GU112311 (Blokhuis et al. 2010) Mamu-KIR3DL04 Mamu-KIR3DL04*001:03 None GU112319 (Blokhuis et al. 2010) Mamu-KIR3DL04 Mamu-KIR3DL04*002 KIR3DL11*003-BNB EU419042 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*001 KIR3DL16*001-BNB EU419045 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*002 KIR3DL7*004-BNB EU419061 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*003 KIR3DL7*005-BNB EU419062 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*004 KIR3DL7*009-BNB EU419066 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*005 KIR3DL7*013-BNB EU419069 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*006:01 KIR3DL7-like2 EU688991 (Moreland et al. 2011) Mamu-KIR3DL05 Mamu-KIR3DL05*006:02 None GU112293 (Blokhuis et al. 2010) Mamu-KIR3DL05 Mamu-KIR3DL05*007 KIR3DL-3 FN424252 (Kruse et al. 2010) Mamu-KIR3DL05 Mamu-KIR3DL05*008 3DL7b-3DL40 GU112291, GU014295 (Blokhuis et al. 2010) (Colantonio et al. 2011) 576 Immunogenetics (2018) 70:571–583 Table 4 (continued) Gene Allele designation Previous designations Accession number Reference Mamu-KIR3DL05 Mamu-KIR3DL05*009 None GU112310 (Blokhuis et al. 2010) Mamu-KIR3DL05 Mamu-KIR3DL05*010 KIR3DL allele 13 FJ562120 (Bostik et al. 2009) Mamu-KIR3DL05 Mamu-KIR3DL05*011 KIR3DL allele 14 FJ562121 (Bostik et al. 2009) Mamu-KIR3DL06 Mamu-KIR3DL06*001 KIR3DL6 AF334621 (Hershberger et al. 2001) Mamu-KIR3DL06 Mamu-KIR3DL06*002 KIR3DL6*001-BNB EU419056 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*001 KIR3DL7 AF334622 (Hershberger et al. 2001) Mamu-KIR3DL07 Mamu-KIR3DL07*002 KIR3DL18 AF361086 (Grendell et al. 2001) Mamu-KIR3DL07 Mamu-KIR3DL07*003 KIR3DL7*001-BNB EU419057 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*004 KIR3DL7*003-BNB EU419060 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*005 KIR3DL7*006-BNB EU419063 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*006 KIR3DL7*007-BNB EU419064 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*007 KIR3DL7*008-BNB EU419065 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*008 KIR3DL7*012-BNB EU419068 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*009:01 KIR3DL7-like1, 2DL420 EU688990, GU299489 (Colantonio et al. 2011; Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*009:02 None GU112282 (Blokhuis et al. 2010) Mamu-KIR3DL07 Mamu-KIR3DL07*010 KIR3DL7-like3 EU688992 (Moreland et al. 2011) Mamu-KIR3DL07 Mamu-KIR3DL07*011 KIR3DL allele 10 FJ562117 (Bostik et al. 2009) Mamu-KIR3DL07 Mamu-KIR3DL07*012 KIR3DL allele 11 FJ562118 (Bostik et al. 2009) Mamu-KIR3DL08 Mamu-KIR3DL08*001:01 KIR3DL8 AY728189 (Sambrook et al. 2005) Mamu-KIR3DL08 Mamu-KIR3DL08*001:02 KIR3DL8*002-BNB EU419071 (Moreland et al. 2011) Mamu-KIR3DL08 Mamu-KIR3DL08*002 KIR3DL17 AF361084, GU112306 (Blokhuis et al. 2010; Grendell et al. 2001) Mamu-KIR3DL08 Mamu-KIR3DL08*003 KIR3DL17 AF361085 (Grendell et al. 2001) Mamu-KIR3DL08 Mamu-KIR3DL08*004 KIR3DL-like_2 AY505477 (Andersen et al. 2004) Mamu-KIR3DL08 Mamu-KIR3DL08*005 KIRDL8 AY728189 (Sambrook et al. 2005) R3DL08 Mamu-KIR3DL08*006 KIR3DL8*001-BNB EU419070 (Moreland et al. 2011) Mamu-KI Mamu-KIR3DL08 Mamu-KIR3DL08*007 None GU112268 (Blokhuis et al. 2010) Mamu-KIR3DL08 Mamu-KIR3DL08*008 None GU112285 (Blokhuis et al. 2010) Mamu-KIR3DL08 Mamu-KIR3DL08*009 None GU112290 (Blokhuis et al. 2010) Mamu-KIR3DL08 Mamu-KIR3DL08*010 None GU112330 (Blokhuis et al. 2010) Mamu-KIR3DL08 Mamu-KIR3DL08*011 KIR3DL allele 8 FJ562115 (Bostik et al. 2009) Mamu-KIR3DL10 Mamu-KIR3DL10*001 KIR3DL10 AY728183 (Sambrook et al. 2005) Mamu-KIR3DL10 Mamu-KIR3DL10*002:01 KIR3DL9, KIR3DL allele 5 AF334624, GU112259, (Hershberger et al. FJ562112 2001)(Blokhuis et al. 2010; Bostik et al. 2009) Mamu-KIR3DL10 Mamu-KIR3DL10*002:02 3DL3NK GU299486 (Colantonio et al. 2011) Mamu-KIR3DL10 Mamu-KIR3DL10*003 KIR3DL10*001-BNB EU419038 (Moreland et al. 2011) Mamu-KIR3DL10 Mamu-KIR3DL10*004 KIR3DL10*002-BNB EU419039 (Moreland et al. 2011) Mamu-KIR3DL10 Mamu-KIR3DL10*005:01 3DL10-2DL501 GU014294 (Colantonio et al. 2011) Mamu-KIR3DL10 Mamu-KIR3DL10*005:02 None GU112295 (Blokhuis et al. 2010) Mamu-KIR3DL10 Mamu-KIR3DL10*006 KIR3DL allele 6 FJ562113 (Bostik et al. 2009) Mamu-KIR3DL11 Mamu-KIR3DL11*001 KIR3DL11 AF334626, GU112271 (Blokhuis et al. 2010; Hershberger et al. 2001) Mamu-KIR3DL11 Mamu-KIR3DL11*002 KIR3DL-1 FN424250 (Kruse et al. 2010) Mamu-KIR3DL11 Mamu-KIR3DL11*003 KIR3DL-6 FN424259 (Kruse et al. 2010) Mamu-KIR3DL11 Mamu-KIR3DL11*004 KIR3DL-7 FN424261 (Kruse et al. 2010) Mamu-KIR3DL11 Mamu-KIR3DL11*005 None GU112276 (Blokhuis et al. 2010) Mamu-KIR3DL11 Mamu-KIR3DL11*006 None GU112296 (Blokhuis et al. 2010) Mamu-KIR3DL11 Mamu-KIR3DL11*007 KIR3DL allele 9 FJ562116 (Bostik et al. 2009) Immunogenetics (2018) 70:571–583 577 Table 4 (continued) Gene Allele designation Previous designations Accession number Reference Mamu-KIR3DL20 Mamu-KIR3DL20*001 KIR3DL20*001-BNB EU419047 (Moreland et al. 2011) Mamu-KIR3DL20 Mamu-KIR3DL20*002 KIR3DL20 AY728184, GU112327 (Blokhuis et al. 2010; Sambrook et al. 2005) Mamu-KIR3DL20 Mamu-KIR3DL20*003 KIR3DL20_variant_2 AY728186 (Sambrook et al. 2005) Mamu-KIR3DL20 Mamu-KIR3DL20*004 KIR3DL20*003-BNB EU419048 (Moreland et al. 2011) Mamu-KIR3DL20 Mamu-KIR3DL20*005 KIR3DL20*004-BNB EU419049 (Moreland et al. 2011) Mamu-KIR3DL20 Mamu-KIR3DL20*006 None GU112255 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*007 None GU112256 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*008 None GU112264 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*009 None GU112270 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*010 None GU112275 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*011 None GU112289 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*012 None GU112299 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*013 None GU112304, GU112317 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*014 None GU112308 (Blokhuis et al. 2010) Mamu-KIR3DL20 Mamu-KIR3DL20*015 None GU134802 (Blokhuis et al. 2010) Mamu-KIR3DS01 Mamu-KIR3DS01*001:01 KIR3DH5 AF361087 (Grendell et al. 2001) Mamu-KIR3DS01 Mamu-KIR3DS01*001:02 None GU112307 (Blokhuis et al. 2010) Mamu-KIR3DS01 Mamu-KIR3DS01*002 KIR3DH1 AY728190 (Sambrook et al. 2005) Mamu-KIR3DS01 Mamu-KIR3DS01*003 KIR3DH-7 GU564161 (Chaichompoo et al. 2010) Mamu-KIR3DS02 Mamu-KIR3DS02*001 KIR3DH2 AF334649 (Hershberger et al. 2001) Mamu-KIR3DS02 Mamu-KIR3DS02*002 KIR3DH-like_5 AY505483 (Andersen et al. 2004) Mamu-KIR3DS02 Mamu-KIR3DS02*003 KIR3DH-like_6 AY505484 (Andersen et al. 2004) Mamu-KIR3DS02 Mamu-KIR3DS02*004:01 KIR3DH2*001-BNB, KIR3DH14 EU419026, EU702460 (Blokhuis et al. 2009a; Moreland et al. 2011) Mamu-KIR3DS02 Mamu-KIR3DS02*004:02 KIR3DH13, 3DH42 EU702459, GU014296 (Blokhuis et al. 2009a) (Colantonio et al. 2011) mu-KIR3DS02 Mamu-KIR3DS02*004:03 KIR3DH12 EU702458 (Blokhuis et al. 2009a) Ma Mamu-KIR3DS02 Mamu-KIR3DS02*005 KIR3DH2*002-BNB EU419027 (Moreland et al. 2011) Mamu-KIR3DS02 Mamu-KIR3DS02*006 KIR3DH16 EU702462 (Blokhuis et al. 2009a) Mamu-KIR3DS02 Mamu-KIR3DS02*007 KIR3DH15 EU702461 (Blokhuis et al. 2009a) Mamu-KIR3DS02 Mamu-KIR3DS02*008 KIR3DH10 EU702456, GU112278 (Blokhuis et al. 2009a; Blokhuis et al. 2010) Mamu-KIR3DS02 Mamu-KIR3DS02*009 None GU112261, GU112315 (Blokhuis et al. 2010) Mamu-KIR3DS02 Mamu-KIR3DS02*010 None GU112297 (Blokhuis et al. 2010) Mamu-KIR3DS02 Mamu-KIR3DS02*011 None GU112323 (Blokhuis et al. 2010) Mamu-KIR3DS02 Mamu-KIR3DS02*012 3DH2*NEW1 JN613291 (Hellmann et al. 2011) Mamu-KIR3DS02 Mamu-KIR3DS02*013 3DH2*NEW1 JN613299 (Hellmann et al. 2011) Mamu-KIR3DS03 Mamu-KIR3DS03*001:01 KIR3DH3 AF334650, GU112312 (Hershberger et al. 2001) (Blokhuis et al. 2010) Mamu-KIR3DS03 Mamu-KIR3DS03*001:02 None GU112294 (Blokhuis et al. 2010) Mamu-KIR3DS03 Mamu-KIR3DS03*002 KIR3DH9 EU702455, GU112269 (Blokhuis et al. 2009a; Blokhuis et al. 2010) Mamu-KIR3DS03 Mamu-KIR3DS03*003 KIR3DH8 EU702454 (Blokhuis et al. 2009a) Mamu-KIR3DS04 Mamu-KIR3DS04*001 KIR3DH4 AF334651 (Hershberger et al. 2001) Mamu-KIR3DS04 Mamu-KIR3DS04*002 KIR3DH4*001-BNB EU419028 (Moreland et al. 2011) Mamu-KIR3DS04 Mamu-KIR3DS04*003 KIR3DH4*002-BNB, KIR3DH4 EU419029, JN613296 (Hellmann et al. 2011; Moreland et al. 2011) Mamu-KIR3DS04 Mamu-KIR3DS04*004 KIR3DH6 EU702452 (Blokhuis et al. 2009a) Mamu-KIR3DS04 Mamu-KIR3DS04*005 KIR3DH4 JN613300 (Hellmann et al. 2011) 578 Immunogenetics (2018) 70:571–583 Table 4 (continued) Gene Allele designation Previous designations Accession number Reference Mamu-KIR3DS04 Mamu-KIR3DS04*006 KIR3DH-1 GU564157 (Chaichompoo et al. 2010) Mamu-KIR3DS05 Mamu-KIR3DS05*001 KIR3DH1*001-BNB EU419024, EU419025, (Moreland et al. 2011) EU702468, AY505487, GU112262 Mamu-KIR3DS05 Mamu-KIR3DS05*002:01 KIR3DH1*002-BNB, KIR3DM1, EU419025, EU702468, (Andersen et al. 2004; KIR_Partial_Sequence_1 AY505487, GU112262 Blokhuis et al. 2009a; Blokhuis et al. 2010; Moreland et al. 2011) Mamu-KIR3DS05 Mamu-KIR3DS05*002:02 KIR3DM6 EU702473 (Blokhuis et al. 2009a) Mamu-KIR3DS05 Mamu-KIR3DS05*003 KIR3DM-1 FN424260 (Kruse et al. 2010) Mamu-KIR3DS06 Mamu-KIR3DS06*001 KIR3DH-like_7 AY505485 (Andersen et al. 2004) Mamu-KIR3DS06 Mamu-KIR3DS06*002:01 KIR3DH-like8 EU688985 (Moreland et al. 2011) Mamu-KIR3DS06 Mamu-KIR3DS06*002:02 None GU112298 (Blokhuis et al. 2010) Mamu-KIR3DS06 Mamu-KIR3DS06*003 KIR3DH18 EU702464 (Blokhuis et al. 2009a) Mamu-KIR3DS06 Mamu-KIR3DS06*004 KIR3DH-4 FN424257 (Kruse et al. 2010) Mamu-KIR3DS06 Mamu-KIR3DS06*005 None GU112260 (Blokhuis et al. 2010) Mamu-KIR3DS06 Mamu-KIR3DS06*006 None GU112314 (Blokhuis et al. 2010) Mamu-KIR3DSW07 Mamu-KIR3DSW07*001 KIR3DH7 EU702453, GU112272 (Blokhuis et al. 2009a; Blokhuis et al. 2010) Mamu-KIR3DSW07 Mamu-KIR3DSW07*002 KIR3DH-5 FN424258 (Kruse et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*001 KIR3DH-like_1 AY505479 (Andersen et al. 2004) Mamu-KIR3DSW08 Mamu-KIR3DSW08*002 KIR3DH-like_2 AY505480 (Andersen et al. 2004) Mamu-KIR3DSW08 Mamu-KIR3DSW08*003 KIR3DH-like_3 AY505481 (Andersen et al. 2004) Mamu-KIR3DSW08 Mamu-KIR3DSW08*004 KIR3DH-like_4 AY505482 (Andersen et al. 2004) Mamu-KIR3DSW08 Mamu-KIR3DSW08*005 KIR3DH21 EU702467 (Blokhuis et al. 2009a) Mamu-KIR3DSW08 Mamu-KIR3DSW08*006 KIR3DH-2 FN424254 (Kruse et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*007 KIR3DH-3 FN424255 (Kruse et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*008 None GU112325 (Blokhuis et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*009 None GU112328 (Blokhuis et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*010 KIR3DSW08 JN613297 (Hellmann et al. 2011) Mamu-KIR3DSW08 Mamu-KIR3DSW08*011 KIR3DH-4 GU564158 (Chaichompoo et al. 2010) Mamu-KIR3DSW08 Mamu-KIR3DSW08*012 KIR3DH-5 GU564159 (Chaichompoo et al. 2010) Mamu-KIR3DSW09 Mamu-KIR3DSW09*001 KIR3DH5*001-BNB EU419030 (Moreland et al. 2011) Mamu-KIR3DSW09 Mamu-KIR3DSW09*002 KIR3DH5-like1 EU688986 (Moreland et al. 2011) Mamu-KIR3DSW09 Mamu-KIR3DSW09*003 None GU112301 (Blokhuis et al. 2010) Mamu-KIR3DSW09 Mamu-KIR3DSW09*004 KIR3DH20 EU702466, GU112273 (Blokhuis et al. 2009a), (Blokhuis et al. 2010) Mamu-KIR3DSW09 Mamu-KIR3DSW09*005 mmKIR3DH-1 FN424249 (Kruse et al. 2010) Mamu-KIR3DSW09 Mamu-KIR3DSW09*006 KIR3DH-8 GU564162 (Chaichompoo et al. 2010) Mamu-KIR3DLX1 Mamu-KIR3DLX1*001 KIR3DL0 DQ157756 (Sambrook et al. 2006) the sequence originally named Mamu-KIR3DL5 (Hershberger primate lineage 1 KIR, referred to as 2DL4 and has been et al. 2001) is a recombinant of Mamu-KIR3DL01 and Mamu- named Mamu-KIR2DL04. A single lineage III KIR is also KIR3DL07. As such, it has been renamed as an allele of present on some Mamu-KIR haplotypes and in all cases Mamu-KIR3DL01, Mamu-KIR3DL01*005. This principal appears to be expressed as a one Ig domain KIR. It has been has also been applied to recombinant alleles in other species. named Mamu-KIR1D. Finally, there is a lineage V KIR gene Along with the lineage II KIR genes, rhesus macaques that is expressed as either a two Ig or three Ig domain KIR. have KIR genes for lineage I, III, and V KIR. The lineage I The published genomic sequence shows the gene to contain KIR gene in rhesus macaques is orthologous to other three Ig domain encoding exons; however, due to splicing Immunogenetics (2018) 70:571–583 579 Table 5 Allele designations and their previous names Gene Allele designation Previous designations Accession number Reference Patr-KIR2DL4 Patr-KIR2DL4*001 None HM068617 (Abi-Rached et al. 2010) Patr-KIR2DL4 Patr-KIR2DL4*002 None AC155174, AF258804 (Khakoo et al. 2000) Patr-KIR2DL4 Patr-KIR2DL4*003 None BX842589 (Sambrook et al. 2005) Patr-KIR2DL5 Patr-KIR2DL5*001 None HM068617 (Abi-Rached et al. 2010) Patr-KIR2DL5 Patr-KIR2DL5*002 None AF274005 (Rajalingam et al. 2001) Patr-KIR2DL5 Patr-KIR2DL5*003 None AC155174 Patr-KIR2DL5 Patr-KIR2DL5*004 None BX842589 (Sambrook et al. 2005) Patr-KIR2DL5 Patr-KIR2DL5*005 None AF258805 (Khakoo et al. 2000) Patr-KIR2DL6 Patr-KIR2DL6*001 None BX842589, AM292662 (Sambrook et al. 2005) Patr-KIR2DL6 Patr-KIR2DL6*002 None AF258806 Patr-KIR2DL6 Patr-KIR2DL6*003 None AM292661 Patr-KIR2DL7 Patr-KIR2DL7*001 None HM068617 (Abi-Rached et al. 2010) Patr-KIR2DL8 Patr-KIR2DL8*001 None HM068617 (Abi-Rached et al. 2010) Patr-KIR2DL8 Patr-KIR2DL8*002 None AC155174, AM279149 Biassoni, unpublished Patr-KIR2DL8 Patr-KIR2DL8*003 None BX842589 (Sambrook et al. 2005) Patr-KIR2DL9 Patr-KIR2DL9*001 None AC155174 Patr-KIR2DL9 Patr-KIR2DL9*002 None AM292657 Biassoni, unpublished Patr-KIR2DL9 Patr-KIR2DL9*003 None AM400233 Biassoni, unpublished Patr-KIR2DS4 Patr-KIR2DS4*001 None HM068617 Patr-KIR2DS4 Patr-KIR2DS4*002 None AF258807 Patr-KIR3DL1 Patr-KIR3DL1*001:01 None AC155174 Patr-KIR3DL1 Patr-KIR3DL1*001:02 None AF266729 (Rajalingam et al. 2001) Patr-KIR3DL1 Patr-KIR3DL1*002 None BX842589, AF258798 (Sambrook et al. 2005) Patr-KIR3DL1 Patr-KIR3DL1*003 None AF266730 (Rajalingam et al. 2001) Patr-KIR3DL1 Patr-KIR3DL1*004 None AF258799 Patr-KIR3DL1 Patr-KIR3DL1*005 None HM068617 Patr-KIR3DL3 Patr-KIR3DL3*001 None HM068617 Patr-KIR3DL3 Patr-KIR3DL3*002 None BX842589 Patr-KIR3DL3 Patr-KIR3DL3*003 None AC155174 Patr-KIR3DL3 Patr-KIR3DL3*004 None AY327500 Patr-KIR3DL4 Patr-KIR3DL4*001:01 None AM400232 Biassoni, unpublished Patr-KIR3DL4 Patr-KIR3DL4*001:02 None AF258800 (Khakoo et al. 2000) Patr-KIR3DL4 Patr-KIR3DL4*002 None HM068617 (Abi-Rached et al. 2010) Patr-KIR3DL5 Patr-KIR3DL5*001 None AM400235 Biassoni, unpublished Patr-KIR3DL5 Patr-KIR3DL5*003:01 None AF258801 (Khakoo et al. 2000) Patr-KIR3DL5 Patr-KIR3DL5*004 None AC155174, AM292659 Biassoni, unpublished Patr-KIR3DS2 Patr-KIR3DS2*001 None AC155174 Patr-KIR3DS2 Patr-KIR3DS2*002 None AF258803 Patr-KIR3DS6 Patr-KIR3DS6*001 None AM396937 Biassoni, unpublished out of exon 4, also two Ig domain KIR variants are of some of these sequences as Mamu-KIR2DL5.The pres- expressed. The majority of the rhesus macaque gene se- ence of the intact gene as evidenced by the published geno- quence appears orthologous to hominoid KIR3DL3 se- mic sequence, as well as the existence of full-length [three quences, the exception being exon 3 [encoding the D0 do- Ig domain containing] sequences has led us to propose nam- main] which appears more like the hominoid KIR2DL5 se- ing this gene as Mamu-KIR3DL20. This distinguishes this quences. This sequence relationship coupled with the pres- gene from the remaining Mamu-KIR3DL as well as ence of splice variants that lacked exon 4 led to the naming retaining the name of one of the first mRNA sequences that 580 Immunogenetics (2018) 70:571–583 Table 6 Allele designations and their previous names Gene Allele designation Previous designations Accession number Reference Poab-KIR2DL10 Poab-KIR2DL10*001 2DLA AF470358 (Guethlein et al. 2002) Poab-KIR2DL11 Poab-KIR2DL11*001 2DLB EF014479 (Guethlein et al. 2007b) Poab-KIR2DL12 Poab-KIR2DL12*001 2DLC AC200148 Poab-KIR2DL5 Poab-KIR2DL5*001 2DL5 AC200148 Poab-KIR2DS10 Poab-KIR2DS10*001 None AF470364 (Guethlein et al. 2002) Poab-KIR2DS13 Poab-KIR2DS13*001 2DSC1/2DSB AF470362 (Guethlein et al. 2002) Poab-KIR2DS14 Poab-KIR2DS14*001 2DSB/2DSD2 AF470361 (Guethlein et al. 2002) Poab-KIR2DS14 Poab-KIR2DS14*002 2DSA/2DSD1 AF470360 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*001:01 3DLH AF470373 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*001:02 None AC200148 Poab-KIR3DL1 Poab-KIR3DL1*002 3DLC AF470367 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*003 None AF470372 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*004:01 3DLD2 AF470369 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*004:02 3DLD1 EF014479 (Guethlein et al. 2007b) Poab-KIR3DL1 Poab-KIR3DL1*005 3DLA AF470365 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*006 3DLI AF470374 (Guethlein et al. 2002) Poab-KIR3DL1 Poab-KIR3DL1*007 3DLB AF470366 (Guethlein et al. 2002) Poab-KIR3DL3 Poab-KIR3DL3*001 3DL3 AC200148 Poab-KIR3DS1 Poab-KIR3DS1*001 3DS1 AF470375 (Guethlein et al. 2002) Poab-KIRDP Poab-KIRDP*001 DP AC200148 Popy-KIR2DS10 Popy-KIR2DS10*001 2DSD/2DSA AF470364 (Guethlein et al. 2002) Popy-KIR2DS13 Popy-KIR2DS13*001 2DSC2/2DSB AF470363 (Guethlein et al. 2002) Popy-KIR3DL1 Popy-KIR3DL1*001 3DLF AF470372 (Guethlein et al. 2002) Popy-KIR3DL1 Popy-KIR3DL1*002:01 3DLE2 AF470371 (Guethlein et al. 2002) Popy-KIR3DL1 Popy-KIR3DL1*002:02 3DLE1 AF470370 (Guethlein et al. 2002) included all three Ig domain encoding exons, see Table 1 for showed that Pt-KIR3DL3 and KIR3DL1/2 were never present further details. A full list of Mamu-KIR sequences is de- on the same haplotype, Pt-KIR3DL3 was given a different scribedinTable 4. name because it has a distinctive sequence. We are renaming The identification of sequences in other Macaque species the Pt-KIRDl1/2 and Pt-KIR3DL3 as allelic variants of Patr- will follow the same rules, and use the species prefix (Mafa- KIR3DL1, the new name for the framework gene at the KIR, Mane-KIR), and that genes would be named to match telomeric end of the chimpanzee KIR locus. This will allow the closest rhesus gene. the Patr-KIR3DL3 name to be given to the gene previously known as Patr-KIRC1, and which is orthologous to human KIR3DL3, the framework gene at the centromeric end of the Naming chimpanzee KIR genes KIR locus. See Table 2 for further details. A full list of Patr- KIR sequences is described in Table 5. Three studies (Abi-Rached et al. 2010;Khakoo et al. 2000; Sambrook et al. 2005) have described complete sequences of three chimpanzee haplotypes. In addition, the analysis of chim- Naming orangutan KIR genes panzee KIR genotypes has inferred the organization of genes infers the existence of another 17 chimpanzee KIR haplotypes. In the initial description of orangutan KIR cDNA (Guethlein et These analyses have defined 13 different Patr-KIR genes. al. 2002), the sequences were given letter designations be- In all chimpanzee KIR haplotypes, the framework gene at cause their relationships, either alleles or genes, were uncer- the telomeric end is a lineage II KIR gene. Formerly, two tain. Subsequent studies (Guethlein et al. 2007a;Guethlein et variants, now known to occupy this position, were named al. 2017; Locke et al. 2011; Mager et al. 2001)have provided Pt-KIR3DL1/2 and Pt-KIR3DL3. The name Pt-KIR3DL1/2 complete sequences of three orangutan KIR haplotypes, as was given to reflect its close relationship to both human well as genotyping data that has allowed the structures of KIR3DL1 and KIR3DL2. Although segregation analysis two additional KIR haplotypes to be inferred. These genomic Immunogenetics (2018) 70:571–583 581 Table 7 Allele designations and their previous names Gene Allele designation Previous Accession number Breed Reference designations Bota-KIR2DL1 Bota-KIR2DL1*001 KIR2DL1 AY075102,AF490399 UnknownHolstein (McQueen et al. 2002; Storset et al. 2003; Zimin et al. 2009) Bota-KIR2DL1 Bota-KIR2DL1*002 None JX848327 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR2DS1 Bota-KIR2DS1*001N KIR2DS1 JX848328 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR2DS2 Bota-KIR2DS2*001N None JX848329 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR2DS3 Bota-KIR2DS3*001N None JX848330 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR2DXS1 Bota-KIR2DXS1*001 None AF490400 Holstein (Storset et al. 2003) Bota-KIR2DXP1 Bota-KIR2DXP1*001 None JX848331 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR2DXP2 Bota-KIR2DXP2*001 None JX848332 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL1 Bota-KIR3DXL1*001 KIR3DL1 AF490402 Holstein (Storset et al. 2003; Zimin et al. 2009) Bota-KIR3DXL1 Bota-KIR3DXL1*002 None JX848333 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL2 Bota-KIR3DXL2*001 None JX848334 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL3 Bota-KIR3DXL3*001 None JX848335 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL4 Bota-KIR3DXL4*001 KIR3DL2–001 EF197118 Holstein-Freisian (Dobromylskyj and Ellis 2007; Zimin et al. 2009) Bota-KIR3DXL4 Bota-KIR3DXL4*002 None JX848336 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL5 Bota-KIR3DXL5*001 None JX848337 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXL6 Bota-KIR3DXL6*001N KIR3DL1P AY075103JX848338 UnknownHolstein-Freisian (McQueen et al. 2002) (Sanderson et al. 2014) Bota-KIR3DXL6 Bota-KIR3DXL6*002 KIR3DL3 EF197119 Holstein-Freisian (Dobromylskyj and Ellis 2007; Zimin et al. 2009) Bota-KIR3DXL7 Bota-KIR3DXL7*001 None JX848339 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXS1 Bota-KIR3DXS1*001 KIR3DS1 AF490401 Holstein (Storset et al. 2003; Zimin et al. 2009) Bota-KIR3DXS1 Bota-KIR3DXS1*002 KIR3DS1–002 EF197120 Holstein-Freisian (Dobromylskyj and Ellis 2007) Bota-KIR3DXS1 Bota-KIR3DXS1*003 None JX848340 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXS2 Bota-KIR3DXS2*001N None JX848341 Holstein-Freisian (Sanderson et al. 2014) Bota-KIR3DXS3 Bota-KIR3DXS3*001N None JX848342 Holstein-Freisian (Sanderson et al. 2014) data, in combination with the cDNA sequences, defined 11 Ellis 2007; Guethlein et al. 2007a; Hammond et al. 2016; KIR genes and 1 KIR pseudogene in the orangutan. At first, all Mager et al. 2001; Sanderson et al. 2014). This presents the orangutan KIR were named as BPopy^ (Guethlein et al. opportunity to adopt an accurate and logical nomenclature 2007b). The orangutan KIR is now divided into two series system. Cattle KIR cDNA sequences were previously named corresponding to the two species of orangutan: Popy for using the established convention of Ig domain number and tail Pongo pygmaeus and Poab for Pongo abelii depending on length. However, these alleles were annotated prior to the species of origin. Some KIR alleles are present in both orang- discovery of a second deeply divergent KIR lineage, the utan species. These alleles shared have been given a different KIR3DX lineage (Guethlein et al. 2007a). The majority of name in each species (Guethlein et al. 2017; Guethlein et al. the expanded cattle KIR belong to this second lineage. In 2015), see Table 3: for further details. A full list of Popy-KIR developing a nomenclature system for the cattle KIR,we have and Poab-KIR sequences is given in Table 6. incorporate their lineage ancestry within the name. Cattle KIR have been prefixed with a four-letter species designation BBota^ (Bos taurus) in line with non-human primates. Naming cattle KIR genes Where possible previously named Bota-KIR has retained the same name with only the addition of an BX^ after the domain Assembly of the first cattle KIR haplotype allowed previously number if from the KIR3DX lineage. There are three excep- known cDNA sequences to be assigned to particular genes tions; Bota-KIR3DL1P and Bota-KIR3DL3, which are allelic, and allelic relationships to be defined (Dobromylskyj and 582 Immunogenetics (2018) 70:571–583 Fig. 1 Non-human KIR nomenclature. Details the syntax and structure of a non-human KIR allele designation and Bota-KIR3DL2. These previously described cDNA se- References quences are all members of the KIR3DX lineage. Based on their position in the cattle haplotype and their relationships Abi-Rached L, Moesta AK, Rajalingam R, Guethlein LA, Parham P (2010) Human-specific evolution and adaptation led to major qual- to other genes, Bota-KIR3DL1P was renamed Bota- itative differences in the variable receptors of human and chimpan- KIR3DXL6*001N, Bota-KIR3DL3 was renamed Bota- zee natural killer cells. PLoS Genet 6:e1001192 KIR3DXL6*002,and Bota-KIR3DL2 was renamed Bota- Andersen H, Rossio JL, Coalter V, Poore B, Martin MP, Carrington M, KIR3DXL4. We haveidentified16 cattle KIR genes. The pro- Lifson JD (2004) Characterization of rhesus macaque natural killer activity against a rhesus-derived target cell line at the single-cell posed nomenclature for cattle KIR is given in Table 7. level. Cell Immunol 231:85–95 Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Future guidelines Ostell J, Sayers EW (2017) GenBank. Nucleic Acids Res 45: D37–D42 The sequences described in this report will be included in the Blokhuis JH, Doxiadis GG, Bontrop RE (2009a) A splice site mutation converts an inhibitory killer cell Ig-like receptor into an activating Immuno Polymorphism Database (IPD) (Robinson et al. 2013). one. Mol Immunol 46:640–648 They will be maintained as a component of the IPD and be Blokhuis JH, van der Wiel MK, Doxiadis GG, Bontrop RE (2009b) accessible at https://www.ebi.ac.uk/ipd/nhkir/. New sequences Evidence for balancing selection acting on KIR2DL4 genotypes in for any of the above species can be submitted using the current rhesus macaques of Indian origin. Immunogenetics 61:503–512 submission tool. As with the other databases, there are Blokhuis JH, van der Wiel MK, Doxiadis GG, Bontrop RE (2010) The mosaic of KIR haplotypes in rhesus macaques. Immunogenetics 62: requirements that should be met before formal names can be 295–306 given and the submitted KIR are included in the database. First, Bostik P, Kobkitjaroen J, Tang W, Villinger F, Pereira LE, Little DM, submission of full-length sequences is encouraged and for some Stephenson ST, Bouzyk M, Ansari AA (2009) Decreased NK cell species like rhesus macaque is already mandatory. Second, nov- frequency and function is associated with increased risk of KIR3DL allele polymorphism in simian immunodeficiency virus-infected el sequences must be confirmed, either through their replication rhesus macaques with high viral loads. J Immunol 182:3638–3649 in multiple individuals or at a minimum by coming from mul- Chaichompoo P, Bostik P, Stephenson S, Udompunturuk S, Kobkitjaroen tiple independent PCR/cloning experiments. Full guidelines for J, Pattanapanyasat K, Ansari AA (2010) Multiple KIR gene poly- submission of non-human KIR sequences to IPD can be found morphisms are associated with plasma viral loads in SIV-infected at https://www.ebi.ac.uk/ipd/nhkir/submission/help. rhesus macaques. Cell Immunol 263:176–187 Chojnacki S, Cowley A, Lee J, Foix A, Lopez R (2017) Programmatic As KIR sequence data from other species reaches the level access to bioinformatics tools from EMBL-EBI update: 2017. of the species included in this report, those species can be Nucleic Acids Res 45:W550–W553 included in the database. The inclusion of a species will be Colantonio AD, Bimber BN, Neidermyer WJ Jr, Reeves RK, Alter G, at the discretion of the Nomenclature Committee and IPD and Altfeld M, Johnson RP, Carrington M, O'Connor DH, Evans DT will be based on the number of sequences available as well as (2011) KIR polymorphisms modulate peptide-dependent binding to an MHC class I ligand with a Bw6 motif. PLoS Pathog 7: evidence of identified genes and haplotype structure. e1001316 de Groot NG, Otting N, Robinson J, Blancher A, Lafont BA, Marsh Funding JAH and NDS were supported by the United Kingdom SGE, O'Connor DH, Shiina T, Walter L, Watkins DI, Bontrop Biotechnology and Biological Sciences Research Council (BBSRC) RE (2012) Nomenclature report on the major histocompatibility through projects BBS/E/I/00001410 and BBS/E/I/00001710. complex genes and alleles of great ape, old and new world monkey species. Immunogenetics 64:615–631 Open Access This article is distributed under the terms of the Creative Dobromylskyj M, Ellis S (2007) Complexity in cattle KIR genes: tran- Commons Attribution 4.0 International License (http:// scription and genome analysis. 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Journal

ImmunogeneticsSpringer Journals

Published: Jun 4, 2018

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