Vstm5 (V-set and transmembrane domain containing 5) - Rat Genome Database

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Gene: Vstm5 (V-set and transmembrane domain containing 5) Rattus norvegicus
Analyze
Symbol: Vstm5
Name: V-set and transmembrane domain containing 5
RGD ID: 1563328
Description: Predicted to be involved in several processes, including filopodium assembly; positive regulation of excitatory synapse assembly; and protein homooligomerization. Predicted to be located in membrane. Predicted to be active in axon; dendrite; and plasma membrane. Orthologous to human VSTM5 (V-set and transmembrane domain containing 5); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical gene supported by BC088439; hypothetical protein LOC500947; LOC500947; V-set and transmembrane domain-containing protein 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8820,361,474 - 20,381,844 (+)NCBIGRCr8
mRatBN7.2812,080,019 - 12,100,443 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl812,080,203 - 12,100,427 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx816,061,601 - 16,081,949 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0814,359,351 - 14,379,699 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0812,343,161 - 12,363,394 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0813,796,009 - 13,816,125 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl813,796,021 - 13,816,109 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0813,735,551 - 13,755,650 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4812,041,325 - 12,061,557 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera813,547,930 - 13,568,159 (+)NCBICelera
Cytogenetic Map8q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
axon  (IBA,ISO,ISS)
dendrite  (IBA,ISO,ISS)
membrane  (ISO,ISS)
plasma membrane  (IBA,ISO,ISS)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:25826454   PMID:27683913  


Genomics

Comparative Map Data
Vstm5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8820,361,474 - 20,381,844 (+)NCBIGRCr8
mRatBN7.2812,080,019 - 12,100,443 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl812,080,203 - 12,100,427 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx816,061,601 - 16,081,949 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0814,359,351 - 14,379,699 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0812,343,161 - 12,363,394 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0813,796,009 - 13,816,125 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl813,796,021 - 13,816,109 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0813,735,551 - 13,755,650 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4812,041,325 - 12,061,557 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera813,547,930 - 13,568,159 (+)NCBICelera
Cytogenetic Map8q12NCBI
VSTM5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381193,818,232 - 93,850,618 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1193,818,232 - 93,850,618 (-)EnsemblGRCh38hg38GRCh38
GRCh371193,551,398 - 93,583,784 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361193,191,621 - 93,236,793 (-)NCBINCBI36Build 36hg18NCBI36
Celera1190,845,176 - 90,875,111 (-)NCBICelera
Cytogenetic Map11q21NCBI
HuRef1189,630,432 - 89,660,369 (-)NCBIHuRef
CHM1_11193,436,686 - 93,466,625 (-)NCBICHM1_1
T2T-CHM13v2.01193,734,553 - 93,766,945 (-)NCBIT2T-CHM13v2.0
Vstm5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39915,150,197 - 15,170,717 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl915,150,341 - 15,170,712 (+)EnsemblGRCm39 Ensembl
GRCm38915,238,901 - 15,259,421 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl915,239,045 - 15,259,416 (+)EnsemblGRCm38mm10GRCm38
MGSCv37915,043,489 - 15,063,857 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36914,989,438 - 15,009,806 (+)NCBIMGSCv36mm8
Celera912,518,122 - 12,538,679 (+)NCBICelera
Cytogenetic Map9A2NCBI
cM Map94.72NCBI
Vstm5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955414727,528 - 751,379 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955414727,714 - 751,368 (+)NCBIChiLan1.0ChiLan1.0
VSTM5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2994,676,258 - 94,714,711 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11195,772,085 - 95,806,075 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01188,840,020 - 88,873,107 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11192,327,030 - 92,359,082 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1192,327,030 - 92,359,082 (-)Ensemblpanpan1.1panPan2
VSTM5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1216,928,557 - 6,960,603 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl216,928,126 - 6,960,202 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha216,944,668 - 6,976,365 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0217,109,798 - 7,141,579 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1216,896,088 - 6,927,793 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0216,960,456 - 6,992,192 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0217,009,409 - 7,041,057 (+)NCBIUU_Cfam_GSD_1.0
Vstm5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494778,901,700 - 78,903,925 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936674956,378 - 988,269 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936674956,378 - 988,817 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VSTM5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl926,221,073 - 26,245,395 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1926,221,065 - 26,245,848 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2929,853,128 - 29,879,536 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VSTM5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1185,065,587 - 85,101,467 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl185,067,926 - 85,100,694 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604340,700,282 - 40,734,579 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vstm5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473538,455,821 - 38,502,864 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vstm5
166 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:241
Count of miRNA genes:153
Interacting mature miRNAs:184
Transcripts:ENSRNOT00000013927
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat

Markers in Region
RH134821  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2812,100,136 - 12,100,351 (+)MAPPERmRatBN7.2
Rnor_6.0813,815,819 - 13,816,033NCBIRnor6.0
Rnor_5.0813,755,349 - 13,755,563UniSTSRnor5.0
RGSC_v3.4812,061,256 - 12,061,470UniSTSRGSC3.4
Celera813,567,858 - 13,568,072UniSTS
RH 3.4 Map8111.6UniSTS
Cytogenetic Map8q12UniSTS
BF402330  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2812,081,637 - 12,081,807 (+)MAPPERmRatBN7.2
Rnor_6.0813,797,456 - 13,797,625NCBIRnor6.0
Rnor_5.0813,736,986 - 13,737,155UniSTSRnor5.0
RGSC_v3.4812,042,760 - 12,042,929UniSTSRGSC3.4
Celera813,549,365 - 13,549,534UniSTS
RH 3.4 Map8111.8UniSTS
Cytogenetic Map8q12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 14 1
Low 2 10 14 8 6 8 60 34 29 10
Below cutoff 1 28 29 19 13 19 8 10 8 1 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013927   ⟹   ENSRNOP00000013927
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl812,080,203 - 12,100,427 (+)Ensembl
Rnor_6.0 Ensembl813,796,021 - 13,816,109 (+)Ensembl
RefSeq Acc Id: NM_001144870   ⟹   NP_001138342
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8820,361,608 - 20,381,839 (+)NCBI
mRatBN7.2812,080,203 - 12,100,438 (+)NCBI
Rnor_6.0813,796,021 - 13,816,120 (+)NCBI
Rnor_5.0813,735,551 - 13,755,650 (+)NCBI
RGSC_v3.4812,041,325 - 12,061,557 (+)RGD
Celera813,547,930 - 13,568,159 (+)RGD
Sequence:
RefSeq Acc Id: XM_039081905   ⟹   XP_038937833
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8820,361,474 - 20,381,844 (+)NCBI
mRatBN7.2812,080,019 - 12,100,443 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001138342 (Get FASTA)   NCBI Sequence Viewer  
  XP_038937833 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88439 (Get FASTA)   NCBI Sequence Viewer  
  EDL78453 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000013927
  ENSRNOP00000013927.4
  ENSRNOP00055009163
  ENSRNOP00060007456
  ENSRNOP00065014209
GenBank Protein Q5M7U7 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001138342   ⟸   NM_001144870
- Peptide Label: precursor
- UniProtKB: Q5M7U7 (UniProtKB/Swiss-Prot),   A6JNB3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000013927   ⟸   ENSRNOT00000013927
RefSeq Acc Id: XP_038937833   ⟸   XM_039081905
- Peptide Label: isoform X1
Protein Domains
Ig-like C2-type   Natural killer cell receptor 2B4 immunoglobulin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5M7U7-F1-model_v2 AlphaFold Q5M7U7 1-199 view protein structure

Transcriptome

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

Promoters
RGD ID:13695751
Promoter ID:EPDNEW_R6274
Type:single initiation site
Name:Vstm5_1
Description:V-set and transmembrane domain containing 5
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_6.0813,796,091 - 13,796,151EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563328 AgrOrtholog
BioCyc Gene G2FUF-31669 BioCyc
Ensembl Genes ENSRNOG00000010480 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055007044 UniProtKB/Swiss-Prot
  ENSRNOG00060006008 UniProtKB/Swiss-Prot
  ENSRNOG00065011447 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000013927 ENTREZGENE
  ENSRNOT00000013927.7 UniProtKB/Swiss-Prot
  ENSRNOT00055011631 UniProtKB/Swiss-Prot
  ENSRNOT00060009936 UniProtKB/Swiss-Prot
  ENSRNOT00065018591 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7126159 IMAGE-MGC_LOAD
InterPro Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NK_rcpt_2B4_Ig_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:500947 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:95080 IMAGE-MGC_LOAD
NCBI Gene 500947 ENTREZGENE
PANTHER SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V-SET AND TRANSMEMBRANE DOMAIN-CONTAINING PROTEIN 5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Receptor_2B4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vstm5 PhenoGen
RatGTEx ENSRNOG00000010480 RatGTEx
  ENSRNOG00055007044 RatGTEx
  ENSRNOG00060006008 RatGTEx
  ENSRNOG00065011447 RatGTEx
Superfamily-SCOP Immunoglobulin UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6JNB3 ENTREZGENE, UniProtKB/TrEMBL
  Q5M7U7 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Vstm5  V-set and transmembrane domain containing 5  LOC500947  hypothetical gene supported by BC088439  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC500947  hypothetical gene supported by BC088439      Symbol and Name status set to provisional 70820 PROVISIONAL