Vstm4 (V-set and transmembrane domain containing 4) - Rat Genome Database

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Gene: Vstm4 (V-set and transmembrane domain containing 4) Rattus norvegicus
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Symbol: Vstm4
Name: V-set and transmembrane domain containing 4
RGD ID: 1310423
Description: Predicted to act upstream of or within several processes, including endothelial cell proliferation; retina blood vessel maintenance; and vasculature development. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in membrane. Orthologous to human VSTM4 (V-set and transmembrane domain containing 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; alpha-Zearalanol; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC361112; LOC361112; MGC116224; RGD1310423; similar to hypothetical protein FLJ31737; V-set and transmembrane domain-containing protein 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8168,126,630 - 8,206,556 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl168,122,355 - 8,206,549 (+)EnsemblGRCr8
mRatBN7.2168,120,336 - 8,200,272 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl168,120,336 - 8,200,269 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx168,139,159 - 8,219,133 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0169,284,061 - 9,364,032 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0168,131,723 - 8,212,459 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0169,088,142 - 9,172,855 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl169,092,302 - 9,172,888 (+)Ensemblrn6Rnor6.0
Rnor_5.01611,044,275 - 11,135,821 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4168,381,247 - 8,462,917 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera167,005,902 - 7,085,420 (-)NCBICelera
RGSC_v3.1168,381,244 - 8,462,915 (+)NCBI
Cytogenetic Map16p16NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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:12477932  


Genomics

Comparative Map Data
Vstm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8168,126,630 - 8,206,556 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl168,122,355 - 8,206,549 (+)EnsemblGRCr8
mRatBN7.2168,120,336 - 8,200,272 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl168,120,336 - 8,200,269 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx168,139,159 - 8,219,133 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0169,284,061 - 9,364,032 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0168,131,723 - 8,212,459 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0169,088,142 - 9,172,855 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl169,092,302 - 9,172,888 (+)Ensemblrn6Rnor6.0
Rnor_5.01611,044,275 - 11,135,821 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4168,381,247 - 8,462,917 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera167,005,902 - 7,085,420 (-)NCBICelera
RGSC_v3.1168,381,244 - 8,462,915 (+)NCBI
Cytogenetic Map16p16NCBI
VSTM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381049,014,236 - 49,115,522 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1049,014,236 - 49,115,522 (-)Ensemblhg38GRCh38
GRCh371050,222,281 - 50,323,567 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361049,896,258 - 49,993,565 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341049,980,222 - 49,993,560NCBI
Celera1043,807,921 - 43,909,146 (-)NCBICelera
Cytogenetic Map10q11.23NCBI
HuRef1044,558,880 - 44,588,434 (-)NCBIHuRef
HuRef1044,487,160 - 44,537,600 (-)NCBIHuRef
CHM1_11050,504,132 - 50,605,365 (-)NCBICHM1_1
T2T-CHM13v2.01049,863,442 - 49,964,410 (-)NCBIT2T-CHM13v2.0
Vstm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391432,578,713 - 32,661,448 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1432,578,713 - 32,661,448 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381432,856,756 - 32,939,491 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1432,856,756 - 32,939,491 (+)Ensemblmm10GRCm38
MGSCv371433,669,942 - 33,752,675 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361431,685,848 - 31,768,581 (+)NCBIMGSCv36mm8
Celera1429,113,807 - 29,199,077 (+)NCBICelera
Cytogenetic Map14BNCBI
cM Map1419.4NCBI
Vstm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555561,086,092 - 1,159,866 (+)Ensembl
ChiLan1.0NW_0049555561,085,826 - 1,160,916 (+)NCBIChiLan1.0ChiLan1.0
VSTM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2861,270,395 - 61,382,441 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11061,275,161 - 61,387,748 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01045,128,625 - 45,240,558 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
VSTM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.128932,483 - 1,026,893 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha281,159,957 - 1,260,990 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0281,107,069 - 1,208,164 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl281,108,160 - 1,283,203 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.128905,327 - 1,006,508 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.028949,430 - 1,050,338 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0281,072,378 - 1,173,413 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Vstm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721379,943,949 - 80,035,472 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367281,146,680 - 1,239,773 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367281,146,800 - 1,239,264 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VSTM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1489,650,744 - 89,739,269 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11489,650,740 - 89,739,263 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21497,445,097 - 97,533,657 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VSTM4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1942,683,887 - 42,825,924 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl942,683,950 - 42,779,480 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660482,444,783 - 2,546,260 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vstm4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624928841,527 - 924,785 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624928847,501 - 924,779 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Vstm4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1138,581,485 - 8,663,646 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vstm4
889 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:567
Count of miRNA genes:268
Interacting mature miRNAs:311
Transcripts:ENSRNOT00000027198
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16423421216278352Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1638712345387123Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133425095Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139568015Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16423421253708481Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16474422249744222Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16423421216278352Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16126734272Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126734272Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16435482249354822Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)1638712345387123Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16423421249757901Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16423421266955197Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16423421216061395Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139568015Rat
631524Bp75Blood pressure QTL 750.05arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)161177108157035Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683908666195506Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338679049757901Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338679026128267Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683908666195506Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683908666195506Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126734272Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16423433317730812Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683908652786090Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683908666195506Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16330168348301683Rat

Markers in Region
RH141292  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2168,199,889 - 8,200,093 (+)MAPPERmRatBN7.2
Rnor_6.0169,172,473 - 9,172,676NCBIRnor6.0
Rnor_5.01611,135,439 - 11,135,642UniSTSRnor5.0
RGSC_v3.4168,462,535 - 8,462,738UniSTSRGSC3.4
Celera167,006,081 - 7,006,284UniSTS
RH 3.4 Map1683.4UniSTS
Cytogenetic Map16p16UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 162 91 90 59 37 59 6 294 137 11 140 74 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000027198   ⟹   ENSRNOP00000027198
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl168,126,535 - 8,185,693 (+)Ensembl
mRatBN7.2 Ensembl168,120,336 - 8,200,269 (+)Ensembl
Rnor_6.0 Ensembl169,092,302 - 9,172,888 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000094048   ⟹   ENSRNOP00000097801
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl168,122,355 - 8,206,549 (+)Ensembl
mRatBN7.2 Ensembl168,126,433 - 8,200,269 (+)Ensembl
RefSeq Acc Id: NM_001029920   ⟹   NP_001025091
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8168,126,630 - 8,206,556 (+)NCBI
mRatBN7.2168,120,336 - 8,200,272 (+)NCBI
Rnor_6.0169,092,307 - 9,172,855 (+)NCBI
Rnor_5.01611,044,275 - 11,135,821 (+)NCBI
RGSC_v3.4168,381,247 - 8,462,917 (+)RGD
Celera167,005,902 - 7,085,420 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001025091 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH98063 (Get FASTA)   NCBI Sequence Viewer  
  EDL88906 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027198
  ENSRNOP00000027198.6
  ENSRNOP00000097801.2
RefSeq Acc Id: NP_001025091   ⟸   NM_001029920
- Peptide Label: precursor
- UniProtKB: Q4QQR8 (UniProtKB/TrEMBL),   A6KFU9 (UniProtKB/TrEMBL),   A0A8I6GM81 (UniProtKB/TrEMBL),   F7F821 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000027198   ⟸   ENSRNOT00000027198
Ensembl Acc Id: ENSRNOP00000097801   ⟸   ENSRNOT00000094048
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4QQR8-F1-model_v2 AlphaFold Q4QQR8 1-319 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699945
Promoter ID:EPDNEW_R10469
Type:initiation region
Name:Vstm4_1
Description:V-set and transmembrane domain containing 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0169,092,211 - 9,092,271EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310423 AgrOrtholog
BioCyc Gene G2FUF-12097 BioCyc
Ensembl Genes ENSRNOG00000020078 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027198 ENTREZGENE
  ENSRNOT00000027198.9 UniProtKB/TrEMBL
  ENSRNOT00000094048.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7458419 IMAGE-MGC_LOAD
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  IgSF_V-set/TM_domain UniProtKB/TrEMBL
KEGG Report rno:361112 UniProtKB/TrEMBL
MGC_CLONE MGC:116224 IMAGE-MGC_LOAD
NCBI Gene 361112 ENTREZGENE
PANTHER V-SET AND TRANSMEMBRANE DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  V-SET AND TRANSMEMBRANE DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
Pfam V-set UniProtKB/TrEMBL
PhenoGen Vstm4 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020078 RatGTEx
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A8I6GM81 ENTREZGENE, UniProtKB/TrEMBL
  A0ABZ3NND3_RAT UniProtKB/TrEMBL
  A6KFU9 ENTREZGENE, UniProtKB/TrEMBL
  F7F821 ENTREZGENE, UniProtKB/TrEMBL
  Q4QQR8 ENTREZGENE
UniProt Secondary Q4QQR8 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Vstm4  V-set and transmembrane domain containing 4  RGD1310423  similar to hypothetical protein FLJ31737  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1310423  similar to hypothetical protein FLJ31737  RGD1310423_predicted  similar to hypothetical protein FLJ31737 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1310423_predicted  similar to hypothetical protein FLJ31737 (predicted)  LOC361112_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361112_predicted  similar to hypothetical protein FLJ31737 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL