Vstm2b (V-set and transmembrane domain containing 2B) - Rat Genome Database

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Gene: Vstm2b (V-set and transmembrane domain containing 2B) Mus musculus
Analyze
Symbol: Vstm2b
Name: V-set and transmembrane domain containing 2B
RGD ID: 1314735
MGI Page MGI
Description: Predicted to be active in membrane. Is expressed in brain and spinal cord mantle layer. Orthologous to human VSTM2B (V-set and transmembrane domain containing 2B).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 2900093B09Rik; AB030198; V-set and transmembrane domain-containing protein 2B
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39740,547,614 - 40,579,468 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl740,547,752 - 40,580,018 (+)EnsemblGRCm39 Ensembl
GRCm38740,898,011 - 40,930,044 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl740,898,328 - 40,930,594 (+)EnsemblGRCm38mm10GRCm38
MGSCv37748,154,648 - 48,185,338 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36740,672,431 - 40,703,121 (+)NCBIMGSCv36mm8
Celera735,862,470 - 35,893,646 (+)NCBICelera
Cytogenetic Map7B3NCBI
cM Map727.88NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:10679242   PMID:11042159   PMID:11076861   PMID:16141072   PMID:16141073   PMID:21267068   PMID:21873635   PMID:25826454   PMID:31847788  


Genomics

Comparative Map Data
Vstm2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39740,547,614 - 40,579,468 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl740,547,752 - 40,580,018 (+)EnsemblGRCm39 Ensembl
GRCm38740,898,011 - 40,930,044 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl740,898,328 - 40,930,594 (+)EnsemblGRCm38mm10GRCm38
MGSCv37748,154,648 - 48,185,338 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36740,672,431 - 40,703,121 (+)NCBIMGSCv36mm8
Celera735,862,470 - 35,893,646 (+)NCBICelera
Cytogenetic Map7B3NCBI
cM Map727.88NCBI
VSTM2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381929,525,418 - 29,564,551 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1929,525,994 - 29,564,551 (+)EnsemblGRCh38hg38GRCh38
GRCh371930,016,325 - 30,055,458 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361934,708,668 - 34,747,070 (+)NCBINCBI36Build 36hg18NCBI36
Celera1926,715,235 - 26,753,005 (+)NCBICelera
Cytogenetic Map19q12NCBI
HuRef1926,528,987 - 26,567,029 (+)NCBIHuRef
CHM1_11930,018,868 - 30,056,624 (+)NCBICHM1_1
T2T-CHM13v2.01932,051,016 - 32,090,146 (+)NCBIT2T-CHM13v2.0
Vstm2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81101,728,708 - 101,757,122 (+)NCBIGRCr8
mRatBN7.2192,592,070 - 92,620,491 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl192,592,070 - 92,620,491 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx197,994,572 - 98,022,973 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01106,460,272 - 106,488,673 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0199,752,857 - 99,781,254 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0197,632,473 - 97,660,962 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl197,632,473 - 97,660,962 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0198,716,586 - 98,744,919 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4192,438,596 - 92,466,532 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1192,404,256 - 92,544,532 (+)NCBI
Celera186,915,860 - 86,944,359 (+)NCBICelera
Cytogenetic Map1q22NCBI
Vstm2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554688,024,159 - 8,054,360 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554688,024,356 - 8,054,229 (-)NCBIChiLan1.0ChiLan1.0
VSTM2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22035,506,775 - 35,545,571 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11937,503,582 - 37,542,293 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01926,454,330 - 26,493,115 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1 Ensembl1935,217,904 - 35,257,097 (+)Ensemblpanpan1.1panPan2
VSTM2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11121,860,643 - 121,879,797 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1121,860,709 - 121,880,030 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1121,163,194 - 121,182,567 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01122,487,392 - 122,506,761 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11122,069,144 - 122,088,519 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01121,676,981 - 121,696,043 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01122,740,755 - 122,760,230 (-)NCBIUU_Cfam_GSD_1.0
Vstm2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244093495,873,610 - 5,898,743 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365705,746,854 - 5,772,272 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365705,747,359 - 5,772,266 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VSTM2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl639,671,131 - 39,700,449 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1639,670,069 - 39,700,473 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2634,963,948 - 34,993,566 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VSTM2B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1624,590,976 - 24,631,921 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl624,592,739 - 24,597,007 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660732,120,476 - 2,159,707 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vstm2b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247944,736,044 - 4,762,221 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247944,736,143 - 4,762,412 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vstm2b
1198 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:109
Count of miRNA genes:99
Interacting mature miRNAs:107
Transcripts:ENSMUST00000044705
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300722Sle3_msystemic lupus erythmatosus susceptibility 3 (mouse)Not determined7351172887142720Mouse
38501068Tip1_mtuberculosis immunophenotype 1, spleen CFU (mouse)7360299972549748Mouse
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76502999133501729Mouse
12792978Fbmd3_mfemoral bone mineral density 3, females only (mouse)77050288142367832Mouse
1357699Nhdlq6_mnon-HDL QTL 6 (mouse)Not determined7998886743988984Mouse
1558893Spir1_mStreptococcus pneumoniae infection resistance 1 (mouse)Not determined71030579844305936Mouse
10449139Eosn1_meosinophil differential 1 (mouse)71248087746480877Mouse
10449158Eosn3_meosinophil differential 3 (mouse)71248087746480877Mouse
4141566Femwf8_mfemur work to failure 8 (mouse)Not determined1303248547032621Mouse
11522751Cocia17_mcocaine-induced activity, QTL 17 (mouse)71313520447135204Mouse
25314314Sccor1_msynaptonemal complex length to mean MLH1 count ratio 1 (mouse)71333392547349748Mouse
1559016Drsi_mDCC-related Spp1 induction (mouse)Not determined71663729349159331Mouse
10412199Sst2_msusceptibility to tuberculosis 2 (mouse)Not determined718728794119485380Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719147398141919804Mouse
1301622Eae12_msusceptibility to experimental allergic encephalomyelitis 12 (mouse)Not determined71928001553280104Mouse
1301052Bhr6_mbronchial hyperresponsiveness 6 (mouse)Not determined71984225053842367Mouse
12904742Litsq2_mlitter size QTL 2 (mouse)72267388756674033Mouse
1301709Bdt4_mbone density traits 4 (mouse)Not determined72288857256888716Mouse
11354952Pdcc1_mplasmacytoid dentritic cell compartment 1 (mouse)72306653157066531Mouse
1301969Lbw5_mlupus NZB x NZW 5 (mouse)Not determined72684761560851775Mouse
12790989Tgl6_mtriglyceride 6 (mouse)72754054961540549Mouse
4141805Sle19_msystematic lupus erythematosus susceptibility 19 (mouse)Not determined3003248581135653Mouse
26884404Huml1_mhumerus length 1, 5 week (mouse)730199425108999207Mouse
1301175Ap7q_malcohol preference 7 QTL (mouse)Not determined73171484565715077Mouse
1300996Aorls2_maortic lesion size 2 (mouse)Not determined73239453266394681Mouse
4142003W3q10_mweight 3 weeks QTL 10 (mouse)Not determined3349772758148965Mouse
4142102Tailq5_mtail length QTL 5 (mouse)Not determined3349772758148965Mouse
4142218W6q17_mweight 6 weeks QTL 17 (mouse)Not determined3349772758148965Mouse
4141909W10q18_mweight 10 weeks QTL 18 (mouse)Not determined3349772758148965Mouse
1357883Epfq5_mepididymal fat pad weight QTL 5 (mouse)Not determined73349772758148965Mouse
1357634Splq7_mspleen weight QTL 7 (mouse)Not determined73349772758148965Mouse
39128210Lwq19_mliver weight QTL 19 (mouse)73349772758148965Mouse
1357469Kidq5_mkidney weight QTL 5 (mouse)Not determined73349772758148965Mouse
1559000Ossc1_mosteosarcoma susceptibility 1 (mouse)Not determined73405302568053223Mouse
38501071Stsl6_mSalmonella typhimurium susceptibility locus 6 (mouse)73419942551149748Mouse
10045622Heal20_mwound healing/regeneration 20 (mouse)Not determined73431688768317043Mouse
1357586Mdmsc3_mmodifier of muscularity 3 (mouse)Not determined73444786968448018Mouse
1301514Rigs1_mradiation induced gastroschisis 1 (mouse)Not determined73628001592394346Mouse
1301082Bbaa16_mB.burgdorferi-associated arthritis 16 (mouse)Not determined736280015116416877Mouse
25314301Vmm3_mvariable multisystem mineralization 3, lung (mouse)73729942572049748Mouse
25314303Vmm4_mvariable multisystem mineralization 4, kidney (mouse)73729942587049208Mouse
1300878Skts1_mskin tumor susceptibility 1 (mouse)Not determined73789138671891582Mouse
10402488Dipa2_mdrug induced psychomotor activation 2 (mouse)Not determined73842154872421684Mouse
1300791Abbp3_mA/J and C57BL/6 blood pressure 3 (mouse)Not determined739673887103510010Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000044705   ⟹   ENSMUSP00000044002
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl740,547,752 - 40,580,018 (+)Ensembl
GRCm38.p6 Ensembl740,898,328 - 40,930,594 (+)Ensembl
RefSeq Acc Id: ENSMUST00000186352   ⟹   ENSMUSP00000140241
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl740,549,553 - 40,552,225 (+)Ensembl
GRCm38.p6 Ensembl740,900,129 - 40,902,801 (+)Ensembl
RefSeq Acc Id: ENSMUST00000205845   ⟹   ENSMUSP00000146231
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl740,548,702 - 40,579,392 (+)Ensembl
GRCm38.p6 Ensembl740,899,278 - 40,929,968 (+)Ensembl
RefSeq Acc Id: ENSMUST00000206223   ⟹   ENSMUSP00000145703
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl740,548,756 - 40,552,212 (+)Ensembl
GRCm38.p6 Ensembl740,899,332 - 40,902,788 (+)Ensembl
RefSeq Acc Id: NM_001418631   ⟹   NP_001405560
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39740,548,184 - 40,579,468 (+)NCBI
RefSeq Acc Id: NM_001418632   ⟹   NP_001405561
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39740,547,614 - 40,579,468 (+)NCBI
RefSeq Acc Id: NM_001418634   ⟹   NP_001405563
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39740,547,614 - 40,579,468 (+)NCBI
RefSeq Acc Id: NM_001418635   ⟹   NP_001405564
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39740,547,614 - 40,579,468 (+)NCBI
RefSeq Acc Id: NM_021387   ⟹   NP_067362
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39740,548,184 - 40,579,468 (+)NCBI
GRCm38740,899,278 - 40,929,968 (+)NCBI
MGSCv37748,154,648 - 48,185,338 (+)RGD
Celera735,862,470 - 35,893,646 (+)RGD
cM Map7 ENTREZGENE
Sequence:
RefSeq Acc Id: NR_184788
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39740,548,184 - 40,579,468 (+)NCBI
RefSeq Acc Id: NR_184789
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39740,548,184 - 40,579,468 (+)NCBI
RefSeq Acc Id: XM_006541032   ⟹   XP_006541095
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39740,548,767 - 40,579,396 (+)NCBI
GRCm38740,899,300 - 40,929,972 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_067362   ⟸   NM_021387
- Peptide Label: isoform 1 precursor
- UniProtKB: Q8CEK5 (UniProtKB/Swiss-Prot),   Q9JME9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006541095   ⟸   XM_006541032
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSMUSP00000140241   ⟸   ENSMUST00000186352
RefSeq Acc Id: ENSMUSP00000145703   ⟸   ENSMUST00000206223
RefSeq Acc Id: ENSMUSP00000146231   ⟸   ENSMUST00000205845
RefSeq Acc Id: ENSMUSP00000044002   ⟸   ENSMUST00000044705
RefSeq Acc Id: NP_001405561   ⟸   NM_001418632
- Peptide Label: isoform 3 precursor
RefSeq Acc Id: NP_001405563   ⟸   NM_001418634
- Peptide Label: isoform 1 precursor
- UniProtKB: Q9JME9 (UniProtKB/Swiss-Prot),   Q8CEK5 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: NP_001405564   ⟸   NM_001418635
- Peptide Label: isoform 2 precursor
RefSeq Acc Id: NP_001405560   ⟸   NM_001418631
- Peptide Label: isoform 2 precursor
Protein Domains
Ig-like   Ig-like V-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JME9-F1-model_v2 AlphaFold Q9JME9 1-285 view protein structure

Promoters
RGD ID:8663719
Promoter ID:EPDNEW_M9891
Type:initiation region
Name:Vstm2b_1
Description:Mus musculus V-set and transmembrane domain containing 2B , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38740,899,284 - 40,899,344EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1914525 AgrOrtholog
Ensembl Genes ENSMUSG00000039257 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000044705 ENTREZGENE
  ENSMUST00000044705.12 UniProtKB/Swiss-Prot
  ENSMUST00000186352.2 UniProtKB/TrEMBL
  ENSMUST00000205845 ENTREZGENE
  ENSMUST00000205845.2 UniProtKB/Swiss-Prot
  ENSMUST00000206223.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_V-set UniProtKB/Swiss-Prot
KEGG Report mmu:58188 UniProtKB/Swiss-Prot
MGD MGI:1914525 ENTREZGENE
NCBI Gene 58188 ENTREZGENE
PANTHER V-SET AND TRANSMEMBRANE DOMAIN-CONTAINING PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V-SET AND TRANSMEMBRANE DOMAIN-CONTAINING PROTEIN 2B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam V-set UniProtKB/Swiss-Prot
PhenoGen Vstm2b PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A087WQL2_MOUSE UniProtKB/TrEMBL
  A0A0U1RNU3_MOUSE UniProtKB/TrEMBL
  Q8CEK5 ENTREZGENE
  Q9JME9 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q8CEK5 UniProtKB/Swiss-Prot