Mouse Chromosome 9
Gene Analysis Unit, Central Institute for Experimental Animals, 1430 Nogawa, Miyamae-ward, Kawasaki 216-0001, Japan
GSF-National Research Center for Environment and Health, Institute of Mammalian Genetics, Ingolstaedter Landstrasse 1, D-85764
Submitted: 1 December 1998
The structure of the Mouse Chromosome 9 Committee Report
(CCR9) is based on a common format agreed among the chromo-
some committee chairpersons at the twelfth International Mouse
Genome Conference in Garmisch, held in October 1998. There are
two versions of CCR9: a printed version in a special issue of
Mammalian Genome and an electronic version deposited in the
Mouse Genome Database (MGD) at The Jackson Laboratory
(http://www.informatics.jax.org). The printed version of CCR9 in-
cludes only Table 1/Map (Locus List) and this Narrative. Addi-
tional information is available for the electronic version, including
a graphical map of mouse chromosome (Chr) 9 (Figure 1) and a
cross table (Table 2).
Chromosome 9 loci
This year’s CCR9 lists a total of 950 valid loci, including 292 of
functional genes or pseudogenes, 64 of EST markers, 555 of
anonymous DNA segment markers, 13 of QTL loci, and 26 of
chromosomal aberrations. Of those, 65 loci are new since the last
CCR9. Forty-eight of the new loci represent new functional genes
or pseudogenes including 27 EST markers. The remaining new
loci include 10 anonymous DNA segment markers as well as seven
QTL locus. Two loci included in the last CCR9, Arha and Rab7,
have been retracted because further mapping data have confirmed
that they map to chromosomes 2 and 6, respectively. D9Mit159
has also been removed from CCR9 as the locus was retracted from
the original MIT map. Some loci are listed as provisional with “S”
for Map Position (MP) because detailed enough mapping infor-
mation was not available by the submission time of this report.
Several locus symbols used in the previous CCR9s are withdrawn
or changed to valid ones. These locus symbols are marked with
“W” and listed separately in Table 1/Map.
Map position (MP) changes
A change of MP to Tgfbr2 (from 52 to 69) has been made based
on re-evaluation of the existing data.
How to use the CCR9 consensus map
The CCR9 consensus map is made by compiling data from a large
number of individual mapping studies. Details of gene order and
positions may be very uncertain on the consensus map, since many
loci have never been mapped with respect to one another in the
same genetic cross, or they have been mapped only by methods
with limited resolutions. In the electronic version of CCR9, the
mapping information is presented in two different formats, which
are meant to be complementary. 1) Graphical maps of Chr 9 (Fig.
1 and a part of Table 1/Map) represent a rough summary of locus
positions based on a large number of different mapping experi-
ments. 2) The Cross Table (Table 2) summarizes the locus order
information that is established by individual mapping studies. Each
column in the table corresponds to an individual genetic cross used
to map three or more loci on Chr 9. For detailed information about
what genes have been mapped with respect to one another in
particular regions, one should consult this table, but not the graphic
map. Readers can also find some conflicts in locus orders deter-
mined by different mapping studies in Table 2. The table lists
seventy crosses, including three crosses that are widely available
interspecific backcrosses; the Jax BSS and BSB crosses, and the
EUCIB crosses. The latest mapping data on these crosses as well
as data on the crosses of Copeland-Jenkins, Kozak, Seldin, and
MIT are available from MGD. Readers can also view mapping
data of a specific locus on other crosses in MGD (Marker Mapping
Other WWW resources
As designated with “H” in the column “Method” of Table 1/Map,
43 STS markers have been included on the T31 radiation hybrid
(RH) map. Updates for the RH data is available at The Jackson
rhmap/rh.html). A number of MIT microsatellite loci, marked with
“P” in the column “Method” of Table 1/Map, have been located on
MIT YACs. Updates for the MIT physical map is available via
internet (http://www.genome.wi.mit.edu). RI/RC strain mapping
data can be downloaded as a set of MapManager files at some web
sites including MGD and Roswell Park (http://mcbio.med.
buffalo.edu). Cytogenetic maps are available from MGD as
graphic files (http://www.informatics.jax.org/cmap.html).
Synteny between mouse Chr 9 and human chromosomes
As of the submission time, 135 human orthologs of mouse Chr 9
genes have been identified and mapped (see Table 1/Map and Fig.
1). A syntenic relationship between mouse Chr 9 and human chro-
mosomes can be best overviewed in Fig. 1. As a rough summary,
mouse Chr 9 segments in an MP range below are homologous to
following human chromosomes (HSA): MP 1-3 to HSA 11, MP
5-7 to HSA 19, MP 8-30 to HSA 11, MP 30-42 to HSA 15, MP
42-48 to HSA 6, MP 50-52 to HSA 15, MP 52-72 to HSA 3.
Acknowledgments. We thank David M. Kingsley for his contributions in
generating earlier Mouse Chromosome 9 Committee Reports on which the
current consensus map is largely based. We also thank Josh Friedman and
David Shaw for their comments on Tgfbr2 and D9Mit159, respectively.
We would appreciate the Informatics Group at The Jackson Laboratory for
the maintenance of the Mouse Genome Database. Access to MGD was
extremely helpful in updating and submitting this report. We apologize for
any omissions or errors, which may exist. We welcome any comments and
corrections from users for future editions of CCR9 (email@example.com).
* Committee Chair
Correspondence to: K. Imai
Mammalian Genome 10, 949 (1999).
© Springer-Verlag New York Inc. 1999