This page provides previous versions of nucleotide polymorphisms of MSM/Ms and JF1/Ms strains, corresponding to GRCm38 coordinate by Liftover from GRCm37.
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RIKEN MSM/Ms Mouse BAC clones & Library
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BAC Information
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Search Result
BAC
Clone Name
MSMg01-237P01
Chromosome
5 (Build37)
Map Location
28,398,978 - 28,399,371
singlet/doublet
singlet
Overlap gene
Insig1
Upstream gene
Dpp6
,
Speer4b
,
Paxip1
,
Htr5a
,
EG433862
,
LOC231069
Downstream gene
En2
,
Cnpy1
,
Prr8
,
Shh
,
LOC100039258
Link
Open Mouse BAC browser
Click to get alignment info.
name
Dpp6
(CDS detail)
type
gene
link
vega
ensembl
MGI
xref
GeneID:13483
MGI:94921
definition
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
name
Speer4b
(CDS detail)
type
gene
link
vega
ensembl
MGI
xref
GeneID:73526
MGI:1920776
definition
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
name
Paxip1
(CDS detail)
type
gene
link
vega
ensembl
MGI
xref
GeneID:55982
MGI:1890430
definition
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
name
Htr5a
(CDS detail)
type
gene
link
vega
ensembl
MGI
xref
GeneID:15563
MGI:96283
definition
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
name
EG433862
(CDS detail)
type
gene
link
vega
ensembl
MGI
xref
GeneID:433862
MGI:3642937
definition
note
: Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 24 ESTs, 19 Proteins
name
LOC231069
(CDS detail)
type
gene
link
vega
ensembl
xref
GeneID:231069
definition
note
: microfibrillar-associated protein 1 pseudogene
pseudo
: _no_value
name
Insig1
(CDS detail)
type
gene
link
vega
ensembl
MGI
xref
GeneID:231070
MGI:1916289
definition
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
name
En2
(CDS detail)
type
gene
link
vega
ensembl
MGI
xref
GeneID:13799
MGI:95390
definition
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
name
Cnpy1
(CDS detail)
type
gene
link
vega
ensembl
MGI
xref
GeneID:269637
MGI:2442451
definition
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
name
Prr8
(CDS detail)
type
gene
link
vega
ensembl
MGI
xref
GeneID:381626
MGI:1919670
definition
note
: Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 3 mRNAs, 149 ESTs, 2 Proteins
name
Shh
(CDS detail)
type
gene
link
vega
ensembl
MGI
xref
GeneID:20423
MGI:98297
definition
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
name
LOC100039258
(CDS detail)
type
gene
link
vega
ensembl
xref
GeneID:100039258
definition
note
: Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 55 mRNAs, 2374 ESTs, 22 Proteins
name
Dpp6
(CDS detail)
type
mRNA
link
vega
ensembl
MGI
NCBI
xref
GI:24429567
GeneID:13483
MGI:94921
definition
exception
: unclassified transcription discrepancy
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
product
: dipeptidylpeptidase 6
transcript_id
: NM_010075.1
name
Speer4b
(CDS detail)
type
mRNA
link
vega
ensembl
MGI
NCBI
xref
GI:21735468
GeneID:73526
MGI:1920776
definition
exception
: unclassified transcription discrepancy
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
product
: spermatogenesis associated glutamate (E)-rich protein 4b
transcript_id
: NM_028561.1
name
Paxip1
(CDS detail)
type
mRNA
link
vega
ensembl
MGI
NCBI
xref
GI:42734450
GeneID:55982
MGI:1890430
definition
exception
: unclassified transcription discrepancy
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
product
: PAX interacting (with transcription-activation domain) protein 1
transcript_id
: NM_018878.2
name
Htr5a
(CDS detail)
type
mRNA
link
vega
ensembl
MGI
NCBI
xref
GI:84370344
GeneID:15563
MGI:96283
definition
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
product
: 5-hydroxytryptamine (serotonin) receptor 5A
transcript_id
: NM_008314.2
name
EG433862
(CDS detail)
type
mRNA
link
vega
ensembl
MGI
NCBI
xref
GI:94374625
GeneID:433862
MGI:3642937
definition
note
: Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 24 ESTs, 19 Proteins
product
: predicted gene, EG433862
transcript_id
: XM_485584.3
name
Insig1
(CDS detail)
type
mRNA
link
vega
ensembl
MGI
NCBI
xref
GI:142378164
GeneID:231070
MGI:1916289
definition
exception
: unclassified transcription discrepancy
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
product
: insulin induced gene 1
transcript_id
: NM_153526.3
name
En2
(CDS detail)
type
mRNA
link
vega
ensembl
MGI
NCBI
xref
GI:142385154
GeneID:13799
MGI:95390
definition
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
product
: engrailed 2
transcript_id
: NM_010134.3
name
Cnpy1
(CDS detail)
type
mRNA
link
vega
ensembl
MGI
NCBI
xref
GI:142369857
GeneID:269637
MGI:2442451
definition
exception
: mismatches in transcription
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
product
: canopy 1 homolog (zebrafish)
transcript_id
: NM_175651.3
name
Prr8
(CDS detail)
type
mRNA
link
vega
ensembl
MGI
NCBI
xref
GI:94374627
GeneID:381626
MGI:1919670
definition
note
: Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 3 mRNAs, 149 ESTs, 2 Proteins
product
: proline rich 8, transcript variant 1
transcript_id
: XM_355585.5
name
Shh
(CDS detail)
type
mRNA
link
vega
ensembl
MGI
NCBI
xref
GI:40254618
GeneID:20423
MGI:98297
definition
exception
: unclassified transcription discrepancy
note
: Derived by automated computational analysis using gene prediction method: BestRefseq. Supporting evidence includes similarity to: 1 mRNA
product
: sonic hedgehog
transcript_id
: NM_009170.2
name
LOC100039258
(CDS detail)
type
mRNA
link
vega
ensembl
NCBI
xref
GI:149253820
GeneID:100039258
definition
note
: Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 39 mRNAs, 1189 ESTs, 22 Proteins
product
: similar to Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), transcript variant 2
transcript_id
: XM_001472557.1
name
LOC100039258
(CDS detail)
type
mRNA
link
vega
ensembl
NCBI
xref
GI:149253818
GeneID:100039258
definition
note
: Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 55 mRNAs, 2372 ESTs, 22 Proteins
product
: similar to Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), transcript variant 1
transcript_id
: XM_001472531.1
name
LOC100039258
(CDS detail)
type
mRNA
link
vega
ensembl
NCBI
xref
GI:149253822
GeneID:100039258
definition
note
: Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 15 mRNAs, 288 ESTs, 2 Proteins
product
: similar to Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), transcript variant 3
transcript_id
: XM_001472580.1
name
Dpp6
(CDS detail)
type
CDS
link
vega
ensembl
MGI
NCBI
xref
GI:24429568
CCDS:CCDS19139.1
GeneID:13483
MGI:94921
definition
codon_start
: 1
note
: inversion, Chr 5, Harwell 6, proximal
product
: dipeptidylpeptidase 6
protein_id
: NP_034205.1
name
Speer4b
(CDS detail)
type
CDS
link
vega
ensembl
MGI
NCBI
xref
GI:21735469
CCDS:CCDS19140.1
GeneID:73526
MGI:1920776
definition
GO_component
: GO:0005575 - cellular_component [Evidence ND]
GO_function
: GO:0003674 - molecular_function [Evidence ND]
GO_process
: GO:0008150 - biological_process [Evidence ND]
codon_start
: 1
note
: sperm-associated glutamate (E)-rich protein 4b; spermatogenic-associated glutamate (E)-rich protein 4b
product
: spermatogenesis associated glutamate (E)-rich protein 4b
protein_id
: NP_082837.1
name
Paxip1
(CDS detail)
type
CDS
link
vega
ensembl
MGI
NCBI
xref
GI:42734451
GeneID:55982
MGI:1890430
definition
GO_component
: GO:0005634 - nucleus [Evidence IDA]
codon_start
: 1
product
: Pax transcription activation domain interacting protein
protein_id
: NP_061366.2
name
Htr5a
(CDS detail)
type
CDS
link
vega
ensembl
MGI
NCBI
xref
GI:84370345
CCDS:CCDS19141.1
GeneID:15563
MGI:96283
definition
GO_component
: GO:0016020 - membrane [Evidence IEA]
GO_function
: GO:0004930 - G-protein coupled receptor activity [Evidence IEA]; GO:0004872 - receptor activity [Evidence IEA]; GO:0001584 - rhodopsin-like receptor activity [Evidence IEA]; GO:0004871 - signal transducer activity [Evidence IEA]
GO_process
: GO:0007186 - G-protein coupled receptor protein signaling pathway [Evidence IEA]; GO:0007165 - signal transduction [Evidence IEA]
codon_start
: 1
product
: 5-hydroxytryptamine receptor 5A
protein_id
: NP_032340.2
name
EG433862
(CDS detail)
type
CDS
link
vega
ensembl
MGI
NCBI
xref
GI:94374626
GeneID:433862
MGI:3642937
definition
codon_start
: 1
product
: hypothetical protein
protein_id
: XP_485584.3
name
Insig1
(CDS detail)
type
CDS
link
vega
ensembl
MGI
NCBI
xref
GI:23943846
CCDS:CCDS19142.1
GeneID:231070
MGI:1916289
definition
GO_component
: GO:0005783 - endoplasmic reticulum [Evidence TAS]; GO:0016020 - membrane [Evidence IEA]
GO_function
: GO:0005515 - protein binding [Evidence IPI]
GO_process
: GO:0006991 - response to sterol depletion [Evidence IDA]
codon_start
: 1
note
: INSIG-1 membrane protein
product
: insulin induced gene 1
protein_id
: NP_705746.1
name
En2
(CDS detail)
type
CDS
link
vega
ensembl
MGI
NCBI
xref
GI:6753752
CCDS:CCDS19143.1
GeneID:13799
MGI:95390
definition
GO_component
: GO:0005634 - nucleus [Evidence IEA]
GO_function
: GO:0003677 - DNA binding [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]; GO:0003700 - transcription factor activity [Evidence IEA]
GO_process
: GO:0007275 - development [Evidence IEA]; GO:0030902 - hindbrain development [Evidence IGI]; GO:0030901 - midbrain development [Evidence IGI]; GO:0048666 - neuron development [Evidence IGI]; GO:0030182 - neuron differentiation [Evidence IGI]; GO:0045449 - regulation of transcription [Evidence IEA]; GO:0006355 - regulation of transcription, DNA-dependent [Evidence IEA]
codon_start
: 1
product
: engrailed 2
protein_id
: NP_034264.1
name
Cnpy1
(CDS detail)
type
CDS
link
vega
ensembl
MGI
NCBI
xref
GI:28316752
CCDS:CCDS19144.1
GeneID:269637
MGI:2442451
definition
codon_start
: 1
product
: canopy 1 homolog
protein_id
: NP_783582.1
name
Prr8
(CDS detail)
type
CDS
link
vega
ensembl
MGI
NCBI
xref
GI:94374628
GeneID:381626
MGI:1919670
definition
codon_start
: 1
product
: proline rich 8 isoform 1
protein_id
: XP_355585.5
name
Shh
(CDS detail)
type
CDS
link
vega
ensembl
MGI
NCBI
xref
GI:21617861
CCDS:CCDS19146.1
GeneID:20423
MGI:98297
definition
GO_component
: GO:0009986 - cell surface [Evidence IDA]; GO:0005615 - extracellular space [Evidence IDA]; GO:0045121 - lipid raft [Evidence IDA]; GO:0016020 - membrane [Evidence IEA]
GO_function
: GO:0016787 - hydrolase activity [Evidence IEA]; GO:0043237 - laminin-1 binding [Evidence IDA]; GO:0005113 - patched binding [Evidence IPI]; GO:0008233 - peptidase activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IPI]
GO_process
: GO:0008209 - androgen metabolism [Evidence IMP]; GO:0001525 - angiogenesis [Evidence IDA]; GO:0007411 - axon guidance [Evidence IDA] [Evidence IMP]; GO:0048754 - branching morphogenesis of a tube [Evidence IMP]; GO:0007154 - cell communication [Evidence IEA]; GO:0048468 - cell development [Evidence IMP]; GO:0001708 - cell fate specification [Evidence IGI] [Evidence IMP]; GO:0007267 - cell-cell signaling [Evidence IMP]; GO:0007417 - central nervous system development [Evidence IMP]; GO:0007275 - development [Evidence IEA]; GO:0009953 - dorsal/ventral pattern formation [Evidence IGI]; GO:0009790 - embryonic development [Evidence IGI]; GO:0042733 - embryonic digit morphogenesis [Evidence IGI]; GO:0030326 - embryonic limb morphogenesis [Evidence IMP]; GO:0048598 - embryonic morphogenesis [Evidence IMP]; GO:0001747 - eye development (sensu Mammalia) [Evidence IDA] [Evidence IMP]; GO:0030900 - forebrain development [Evidence IGI]; GO:0007507 - heart development [Evidence IMP]; GO:0030902 - hindbrain development [Evidence IMP] [Evidence IGI]; GO:0016539 - intein-mediated protein splicing [Evidence IEA]; GO:0030324 - lung development [Evidence IMP] [Evidence IGI]; GO:0030539 - male genitalia development [Evidence IMP]; GO:0001656 - metanephros development [Evidence IMP]; GO:0030901 - midbrain development [Evidence IGI]; GO:0045596 - negative regulation of cell differentiation [Evidence IMP] [Evidence IDA]; GO:0030336 - negative regulation of cell migration [Evidence IDA]; GO:0001755 - neural crest cell migration [Evidence IMP]; GO:0007405 - neuroblast proliferation [Evidence IDA]; GO:0048663 - neuron fate commitment [Evidence IMP]; GO:0014003 - oligodendrocyte development [Evidence IDA]; GO:0009887 - organ morphogenesis [Evidence IMP]; GO:0007389 - pattern specification [Evidence IMP]; GO:0001569 - patterning of blood vessels [Evidence IMP]; GO:0008284 - positive regulation of cell proliferation [Evidence IMP] [Evidence IGI]; GO:0030850 - prostate gland development [Evidence IMP]; GO:0006508 - proteolysis [Evidence IEA]; GO:0042127 - regulation of cell proliferation [Evidence IDA]; GO:0030162 - regulation of proteolysis [Evidence IDA]; GO:0007435 - salivary gland morphogenesis [Evidence IMP]; GO:0007165 - signal transduction [Evidence TAS]; GO:0007224 - smoothened signaling pathway [Evidence IGI] [Evidence IDA]; GO:0051146 - striated muscle cell differentiation [Evidence IMP] [Evidence IDA]; GO:0001658 - ureteric bud branching [Evidence IMP]; GO:0001570 - vasculogenesis [Evidence IDA]
codon_start
: 1
note
: short digits
product
: sonic hedgehog
protein_id
: NP_033196.1
name
LOC100039258
(CDS detail)
type
CDS
link
vega
ensembl
NCBI
xref
GI:149253819
GeneID:100039258
definition
codon_start
: 1
product
: similar to Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) isoform 1
protein_id
: XP_001472581.1
name
LOC100039258
(CDS detail)
type
CDS
link
vega
ensembl
NCBI
xref
GI:149253821
GeneID:100039258
definition
codon_start
: 1
product
: similar to Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) isoform 2
protein_id
: XP_001472607.1
name
LOC100039258
(CDS detail)
type
CDS
link
vega
ensembl
NCBI
xref
GI:149253823
GeneID:100039258
definition
codon_start
: 1
product
: similar to Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) isoform 3
protein_id
: XP_001472630.1
clone name
MSMg01-460N19
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-429O03
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-333M03
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-409L18
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-510N15
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-436E09
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-390N05
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-499E15
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-349M17
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-333A21
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-269P11
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-500J23
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-431D21
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-180J22
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-261O02
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-300L22
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-380M13
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-363G02
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-275D24
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-288P16
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-435A19
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-155B08
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-155B09
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-434G01
singlet/doublet
singlet
plural/unique
plural
clone name
MSMg01-344N20
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-165H08
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-331O14
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-328M12
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-544N11
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-439N23
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-358P20
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-350P20
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-429A07
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-423L11
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-460J02
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-538N09
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-186M21
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-237P01
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-460F20
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-428A20
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-373L03
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-233I13
singlet/doublet
doublet
plural/unique
plural
clone name
MSMg01-270D08
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-512B07
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-324L21
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-404G10
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-072F11
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-498G02
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-380I03
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-479B23
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-491H14
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-421I01
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-352G05
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-407J15
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-435M01
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-288E24
singlet/doublet
doublet
plural/unique
unique
clone name
MSMg01-359D10
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-469N06
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-401E21
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-267K04
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-467G17
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-060D16
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-276P07
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-100L24
singlet/doublet
singlet
plural/unique
unique
clone name
MSMg01-516L15
singlet/doublet
doublet
plural/unique
unique
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doublet
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doublet
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doublet
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