Mouse chromosome 2
23
Mammalian Genome 8, $27-$49 (1998). Mammalian Genome ........ Springer-Verlag New York Inc. 1998 Mouse Chromosome 2 Josephine Peters, 1'* Linda D. Siracusa, 2'** Daniel Pomp, 3 Aamir R. Zuberi, 4 Deanna Church, 5 Revati Koratkar, 2 Catherine M. Abbott 6 1Mammalian Genetics Unit, Medical Research Council, Didcot, Oxon OX11 0RD, UK ajefferson Cancer Center, Jefferson Medical College, Department of Microbiology and Immunology, 233 South 10th Street, Philadelphia, Pennsylvania 19107-5541, USA 3Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0908, USA 4The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA SSamuel Lunenfeld Research Institute, Mt. Sinai Hospital, Rm 884, 600 University Avenue, Toronto, Ontario MG5 1X5, Canada 6Human Genetics Unit, Molecular Medicine Centre, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK Received: 1 December 1997 Introduction This report collates information about the genetic organization of mouse Chromosome 2 (Chr 2). A consensus linkage map of Chr 2 was generated based on a foundation of genetic crosses in which multiple loci were mapped, providing the relative order of loci along the length of the chromosome. The remaining loci were subsequently added to produce a map that serves as a guide for genetic, molecular, and physical analyses. The consensus map is not absolute; locus positions are reassessed each year and may change, since new information is continually integrated into the map. determined and that the estimated location of each locus is inher- ently subject to significant error. Furthermore, evidence suggesting the presence of a QTL may also be indicative of two or more tightly linked loci that cannot be separated statistically. All QTL listed have been detected with forms of interval analysis with significant levels of LOD (3.0 or P < 0.001), or have been con- firmed in multiple crosses or in congenic lines. The electronic version of this report shows a range of position for each QTL listed in Table 1. Identification of YACs that carry Chr 2 markers Locus list Table 1 now lists more than 1100 loci on mouse Chr 2. The asterisk (*) in the first column indicates the new loci assigned to mouse Chr 2 since the last report. Fifty-seven new genes including two new mutations, sooty foot (soo) and ebouriffe (ebo), 91 new DNA markers, and 6 new quantitative trait loci (QTL) have been added. It has been established that pa is not Epb4.2 (38773). The gene for lethal milk was reported to be a zinc transporter (Znt4) at the 1 lth IMGS by Huang and Gitschier. The microsatellite loci, D2Mit301-D2Mit530, have been added; up-to-date listings can be obtained by contacting the Whitehead Institute/MIT Center for Genome Research at http:/www-genome.wi.mit.edu. The D2Cph loci (10555) and D2Ncvs loci (21638) have not yet been included. The consensus map was constructed by first creating a skeleton map based predominantly on multilocus backcross analysis. Data from three and four-point crosses were next incorporated, and loci mapped only in two-point crosses were added last. Placement of loci mapped only in RI strains was estimated by averaging interval distances between flanking markers. Some histocompatibility loci were positioned by analysis of congenic strains. The consensus map should be used as a guide for gene local- ization. Gene order is established unambiguously only for those loci mapped in the same cross. Order for closely linked genes that have not yet been mapped with respect to each other was inferred on the basis of recombination distances. Quantitative trait loci (QTL) Twenty QTL have now been assigned to mouse Chr 2. It is im- portant to note that the true identity of each QTL has not yet been * Chair ** Co-Chair Correspondence to: J. Peters Chr 2 containing YACs are listed in the electronic version of this report. The libraries screened include the Princeton and the origi- nal Whitehead/MIT C57BL/6 YAC libraries, and the combined St. Mary's and ICRF C57BL/10 and C3H libraries (available through the Baylor College of Medicine). Information concerning Chr 2 YACs derived from the more recent Whitehead/MIT-820 C57BL/6 library can be accessed at http://www.informatics.jax. org/mitmaps.html. Comparative maps Mouse Chr 2 shows regions of conserved homology with human Chrs 2, 7, 9, 10, 11, 15, and 20. Table 1 lists the 179 loci mapping to mouse Chr 2 that have also been localized in the human genome, along with their corresponding human gene symbol and human chromosomal location. The Online Mendelian Inheritance in Man database and the Genome DataBase provide references for the mapping of human homologs. Legend for Chromosome Committee Map The information about each locus for a chromosome appears on one line of the map. At the left is a small figure of the whole chromosome. A box on the chromosome figure indicates which portion of the chromosome is expanded for view on that page. To the right of the small figure is the corresponding expanded cen- timorgan scale. For each locus on the chromosome a line extends from the scale to the marker or group of markers at that position. From left-to-right, the columns are: Symbol New an asterisk * appears in the column if this is a newly discovered locus since the last published committee report
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Transcript of Mouse chromosome 2
Mammalian Genome 8, $27-$49 (1998).
Mammal ian Genome ........
�9 Springer-Verlag New York Inc. 1998
Mouse Chromosome 2
Josephine Peters, 1'* Linda D. Siracusa, 2'** Daniel P o m p , 3 A a m i r R. Zuberi , 4 Deanna Church, 5 Revati Koratkar , 2 Catherine M. Abbot t 6
1Mammalian Genetics Unit, Medical Research Council, Didcot, Oxon OX11 0RD, UK ajefferson Cancer Center, Jefferson Medical College, Department of Microbiology and Immunology, 233 South 10th Street, Philadelphia, Pennsylvania 19107-5541, USA 3Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0908, USA 4The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA SSamuel Lunenfeld Research Institute, Mt. Sinai Hospital, Rm 884, 600 University Avenue, Toronto, Ontario MG5 1X5, Canada 6Human Genetics Unit, Molecular Medicine Centre, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
Received: 1 December 1997
Introduction
This report collates information about the genetic organization of mouse Chromosome 2 (Chr 2). A consensus linkage map of Chr 2 was generated based on a foundation of genetic crosses in which multiple loci were mapped, providing the relative order of loci along the length of the chromosome. The remaining loci were subsequently added to produce a map that serves as a guide for genetic, molecular, and physical analyses. The consensus map is not absolute; locus positions are reassessed each year and may change, since new information is continually integrated into the map.
determined and that the estimated location of each locus is inher- ently subject to significant error. Furthermore, evidence suggesting the presence of a QTL may also be indicative of two or more tightly linked loci that cannot be separated statistically. All QTL listed have been detected with forms of interval analysis with significant levels of LOD (3.0 or P < 0.001), or have been con- firmed in multiple crosses or in congenic lines. The electronic version of this report shows a range of position for each QTL listed in Table 1.
Identification of YACs that carry Chr 2 markers
Locus list
Table 1 now lists more than 1100 loci on mouse Chr 2. The asterisk (*) in the first column indicates the new loci assigned to mouse Chr 2 since the last report. Fifty-seven new genes including two new mutations, sooty foot (soo) and ebouriffe (ebo), 91 new DNA markers, and 6 new quantitative trait loci (QTL) have been added. It has been established that pa is not Epb4.2 (38773). The gene for lethal milk was reported to be a zinc transporter (Znt4) at the 1 lth IMGS by Huang and Gitschier. The microsatellite loci, D2Mit301-D2Mit530, have been added; up-to-date listings can be obtained by contacting the Whitehead Institute/MIT Center for Genome Research at http:/www-genome.wi.mit.edu. The D2Cph loci (10555) and D2Ncvs loci (21638) have not yet been included.
The consensus map was constructed by first creating a skeleton map based predominantly on multilocus backcross analysis. Data from three and four-point crosses were next incorporated, and loci mapped only in two-point crosses were added last. Placement of loci mapped only in RI strains was estimated by averaging interval distances between flanking markers. Some histocompatibility loci were positioned by analysis of congenic strains.
The consensus map should be used as a guide for gene local- ization. Gene order is established unambiguously only for those loci mapped in the same cross. Order for closely linked genes that have not yet been mapped with respect to each other was inferred on the basis of recombination distances.
Quantitative trait loci (QTL)
Twenty QTL have now been assigned to mouse Chr 2. It is im- portant to note that the true identity of each QTL has not yet been
* Chair ** Co-Chair Correspondence to: J. Peters
Chr 2 containing YACs are listed in the electronic version of this report. The libraries screened include the Princeton and the origi- nal Whitehead/MIT C57BL/6 YAC libraries, and the combined St. Mary's and ICRF C57BL/10 and C3H libraries (available through the Baylor College of Medicine). Information concerning Chr 2 YACs der ived from the more recent Whi tehead/MIT-820 C57BL/6 library can be accessed at http://www.informatics.jax. org/mitmaps.html.
Comparative maps
Mouse Chr 2 shows regions of conserved homology with human Chrs 2, 7, 9, 10, 11, 15, and 20. Table 1 lists the 179 loci mapping to mouse Chr 2 that have also been localized in the human genome, along with their corresponding human gene symbol and human chromosomal location. The Online Mendelian Inheritance in Man database and the Genome DataBase provide references for the mapping of human homologs.
Legend for Chromosome Committee Map
The information about each locus for a chromosome appears on one line of the map. At the left is a small figure of the whole chromosome. A box on the chromosome figure indicates which portion of the chromosome is expanded for view on that page. To the right of the small figure is the corresponding expanded cen- timorgan scale. For each locus on the chromosome a line extends from the scale to the marker or group of markers at that position. From left-to-right, the columns are:
Symbol New
an asterisk * appears in the column if this is a newly discovered locus since the last published committee report
$28 J. Peters et al.: Mouse Chromosome 2
Confidence of placement on the map filled circles = high confidence, mapping to high resolution in at least one cross with multiple other loci; half-filled circles = intermediate confidence, mapping in one or few crosses relative to one or a few markers; or open circles = low confidence, e.g., mapping by in-situ hybridization only or in a QTL-analysis
Name of locus an asterisk incidates name is truncated at 50 characters
Method of localization L = linkage crosses; I = in-situ hybridization; S = somatic cell hybridization studies; H = radiation cell hybrids; R = RI strain analysis; C = cytogenetic assignment; D = deletion analysis; P = physical mapping; T = partial t-haplotype analy- sis; 0 = other
Trait a 'T ' in the column indicates that the locus has known associ- ated phenotypic traits
Cytogenetic Band Human Homolog
symbol of the human gene if a human homolog is known Human Location
human cytogenetic localization for the homolog up to four Reference Numbers;
in the Mouse Genome Database, reference numbers are of the form J : # ~ ; these numbers represent the ~ # portion of this identifier. Additional references may be available through the Web.
Acknowledgments. Comments on the map are welcomed. We apologize for omissions and respectfully request investigators to send the missing pieces. We thank investigators who generously shared their unpublished results. We thank the staff of the Mouse Genome Database for their help. We are grateful to Rachael Selley for excellent assistance.
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Ref
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hr 2
and
14
Gan
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o-1
reci
proc
al tr
ansl
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ion,
Chr
2 a
nd 1
5, A
dler
-45
reci
proc
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ansl
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Chr
2 a
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9, H
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thal
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4
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body
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TL
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D39
ant
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1
chlo
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chan
nel c
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nt in
duce
r, re
late
d se
puan
c ~
cyst
atln
rel
ated
epi
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mal
spe
cific
D
NA
seg
men
t, C
hr 2
, Birk
enm
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25
DN
A s
egm
ent,
Chr
2, B
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er 2
7, e
xpre
ssed
D
NA
seg
men
t, C
hr 2
, B
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mei
er 2
8, e
xpre
ssed
D
NA
seg
men
t, C
hr 2
, B
ri ha
m &
Wom
an's
Gen
etic
s 01
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NA
seg
men
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hr 2
, Brl
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Chr
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~ D
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seg
men
t, C
hr 2
, Br]
DN
A s
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Chr
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Bri
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A s
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ent,
Chr
2,
Bri
DN
A s
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ent,
Chr
2, B
ri D
NA
seg
men
t, C
hr 2
, Bri
DN
A s
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ent,
Chr
2,
Bri
DN
A s
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Chr
2,
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DN
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Chr
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Bri
ham
& W
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08*
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10"
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13"
ham
& W
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13"
DN
A s
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ent,
Chr
2, B
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m &
Wom
en's
Gen
etic
s 14
" D
NA
seg
men
t, C
hr 2
, Den
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peni
an 1
D
NA
seg
men
t, C
hr 2
, G. C
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lez
1, e
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ssed
D
NA
seg
men
t, C
hr 2
, G. C
onsa
lez
2, e
xpre
ssed
D
NA
seg
men
t, C
hr 2
, G. C
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lez
3, e
xpre
ssed
D
NA
seg
men
t, C
hr 2
, G. C
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4, e
xpre
ssed
D
NA
seg
men
t, C
hr 2
, G. C
onsa
lez
4, e
xpre
ssed
D
NA
seg
men
t, C
hr 2
, P
rince
ton
Uni
vers
;ty 4
D
NA
seg
men
t, C
hr 2
, Ros
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l Par
k 1
DN
A s
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ent,
Chr
2, T
hom
as F
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t 3
DN
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Chr
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Chr
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Chr
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Chr
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as F
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DN
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Chr
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DN
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Chr
2, T
hom
as F
. Vog
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Chr
omos
ome
2 Sy
nten
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arke
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Met
hods
Tr
ail
C
C
C
C
C
I S
L I I L I IL
S LR
I I I C
C
C
C
C
C
C
C
L
T L L
T L L I L L L L L L L L L L L L L L L L L L L L L L L L L L L L L L L L
Ban
d B
&H
1
E4
& H
1 A
1-A
3
H
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E
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2 H
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D
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4 E
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Hom
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PTP
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SP
NR
Ban
d
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3
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3
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lt-p
13
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4-q1
5 9q
34
Ref
eren
ces
3379
9 33
799
3379
9 33
799,
3473
8 33
799
1151
1 31
446,
1611
6 22
229
2311
4 29
59
1822
0 40
71
2211
4,23
729,
2614
0 29
373,
3055
0 64
92
3240
,110
32
1103
3 19
415
2521
9 33
799
1627
0,33
799
3379
9 33
799
3379
9 33
799
2492
7 28
984
5657
24
194
2950
5,30
611
3220
8 32
208
4238
3 39
363
3024
,241
94
2912
6 24
194
2419
4 24
194
2912
6 29
126
2912
6 29
126
2912
5 29
126
2912
6 29
126
2912
5 29
126
2912
6 29
126
2419
4 24
194
2419
4 24
194
2419
4 37
225
3296
2 37
225
3722
5 37
225
3722
5 37
225
3722
5 37
225
rj~
.,-.,
c~
=-
o
Sym
bol
D2T
fvlO
D
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11
D2T
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D
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13
D2T
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D
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15
D2T
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D2T
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D2T
rk3
D2T
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D2W
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le
D2W
sulO
Te
D2W
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7e
D2W
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9e
D2W
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D2W
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3e
D2W
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D2M
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62
D2M
it463
D
2Mit5
08
D2M
it509
D
2Mit5
10
D2M
it511
D
2Mit5
12
D2M
it513
D
2Mit5
14
D2M
it515
D
2Mit5
16
D2M
it517
D
2Mit5
18
D2M
it519
D
2Nds
6 A
qr
Atp
5k.rs
2
New
C
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�9
Nam
e D
NA
seg
men
t, C
hr 2
, Tho
mas
F. V
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0 D
NA
seg
men
t, C
hr 2
, Tho
mas
F. V
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1 D
NA
seg
men
t, C
hr 2
, Tho
mas
F. V
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2 D
NA
seg
men
t, C
hr 2
, Tho
mas
F. V
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3 D
NA
seg
men
t, C
hr 2
, Tho
mas
F. V
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4 D
NA
seg
men
t, C
hr 2
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5 D
NA
seg
men
t, C
hr 2
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1
DN
A s
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Chr
2, T
ular
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D
NA
seg
men
t, C
hr 2
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3
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Chr
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ular
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D
NA
seg
men
t C
hr 2
Way
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D
NA
seg
men
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hr 2
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7, e
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seg
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D
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seg
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43, e
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seg
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x*
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D
NA
seg
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t, C
hr 2
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D
NA
seg
men
t C
hr 2
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ex*
D
NA
seg
men
t, C
hr 2
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Uni
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D
NA
seg
men
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hr 2
, Way
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Uni
vers
ity 68
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mem
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b pu
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and-
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R
yeas
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EC
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DN
A S
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ent,
Chr
2, M
IT 4
60
DN
A S
egm
ent,
Chr
2, M
IT 4
61
DN
A S
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ent,
Chr
2, M
IT 4
62
DN
A S
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ent,
Chr
2, M
IT 4
63
DN
A s
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Chr
2, M
IT 5
08
DN
A s
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Chr
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IT 5
09
DN
A s
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Chr
2, M
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10
DN
A s
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Chr
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IT 5
11
DN
A s
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Chr
2, M
IT 5
12
DN
A s
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Chr
2, M
IT 5
13
DN
A s
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ent,
Chr
2, M
IT 5
14
DN
A s
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Chr
2, M
IT 5
15
DN
A s
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ent,
Chr
2, M
IT 5
16
DN
A s
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Chr
2, M
IT 5
17
DN
A s
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ent,
Chr
2, M
IT 5
18
DN
A s
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ent,
Chr
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19
DN
A s
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Chr
2, N
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ld D
epar
tmen
t of S
urge
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rius
ATP
syn
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+ tra
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chon
dria
l F1F
0*
Chr
omos
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2 Sy
nten
ic M
arke
rs
Met
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Tra
it L L L L L L L L L L L L L L L L L L L L L L L L L L L I L L L L L I L
Ban
d
H3-
H4
Hom
olog
TFA
P2C
Ban
d
2~13
.2
Ref
eren
ces
3722
6 37
225
3722
5 37
225
3722
5 37
225
2912
6 29
126
2912
6 29
126
2912
6 29
126
2912
6 29
126
2912
6 29
126
2912
6 29
126
2912
6 29
126
2912
6 29
126
2912
6 29
126
2912
6 29
126
2912
6 24
194
4246
7 24
194
3637
7,39
185,
3983
0 24
194
2419
4 36
997
2419
4 31
151,
3380
5,35
169
9109
,158
39,3
5638
40
730
4073
0 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 34
136,
3421
2 17
854
2419
4,34
884
P-
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