Vom2r4 (vomeronasal 2 receptor, 4) - Rat Genome Database

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Pathways
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Gene: Vom2r4 (vomeronasal 2 receptor, 4) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Vom2r4
Name: vomeronasal 2 receptor, 4
RGD ID: 1564110
Description: Predicted to enable G protein-coupled receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Predicted to be located in plasma membrane; INTERACTS WITH acrylamide; cadmium dichloride; paraquat.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC108352192; LOC308248; RGD1564110; similar to putative pheromone receptor; vomeronasal 2 receptor 4; vomeronasal type-2 receptor 116-like
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr812,874,499 - 2,889,566 (-)NCBIGRCr8
mRatBN7.21226,465 - 241,532 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1226,341 - 272,253 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1575,935 - 590,998 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.016,576,316 - 6,591,379 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01858,021 - 873,084 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01714,270 - 719,690 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10111,716,966 - 111,735,354 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01703,155 - 708,575 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.411,134,798 - 1,149,865 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera16,347 - 11,772 (-)NCBICelera
Cytogenetic Map1p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)
plasma membrane  (IBA,IEA)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17382427  


Genomics

Variants

.
Variants in Vom2r4
384 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:173
Count of miRNA genes:82
Interacting mature miRNAs:87
Transcripts:ENSRNOT00000043877, ENSRNOT00000048946, ENSRNOT00000070942, ENSRNOT00000071037, ENSRNOT00000072076, ENSRNOT00000072232, ENSRNOT00000073032, ENSRNOT00000074130, ENSRNOT00000074402, ENSRNOT00000074598
Prediction methods:Microtar, Miranda, Rnahybrid
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
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124744506Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128736750Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat


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

endocrine system hemolymphoid system reproductive system respiratory system
High
Medium
Low 3 2
Below cutoff 6 1 25 9

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001099458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000044669   ⟹   ENSRNOP00000043136
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1226,341 - 272,253 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000070942   ⟹   ENSRNOP00000064131
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl10111,716,966 - 111,735,354 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099894   ⟹   ENSRNOP00000090453
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1226,341 - 241,622 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113739   ⟹   ENSRNOP00000081115
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1226,434 - 241,622 (-)Ensembl
RefSeq Acc Id: NM_001099458   ⟹   NP_001092928
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr812,874,499 - 2,889,566 (-)NCBI
mRatBN7.21226,465 - 241,532 (-)NCBI
Rnor_6.01714,270 - 719,690 (-)NCBI
Rnor_5.01703,155 - 708,575 (-)NCBI
RGSC_v3.411,134,798 - 1,149,865 (-)RGD
Celera16,347 - 11,772 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001092928 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000043136.5
  ENSRNOP00000081115.1
  ENSRNOP00000090453
  ENSRNOP00000090453.1
  ENSRNOP00000091616.1
Reference Protein Sequences
RefSeq Acc Id: NP_001092928   ⟸   NM_001099458
- Peptide Label: precursor
- UniProtKB: A0A8I6AEC9 (UniProtKB/TrEMBL),   A0A8I6AFS9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064131   ⟸   ENSRNOT00000070942
RefSeq Acc Id: ENSRNOP00000081115   ⟸   ENSRNOT00000113739
RefSeq Acc Id: ENSRNOP00000043136   ⟸   ENSRNOT00000044669
RefSeq Acc Id: ENSRNOP00000090453   ⟸   ENSRNOT00000099894
Protein Domains
G-protein coupled receptors family 3 profile   Receptor ligand binding region

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R454-F1-model_v2 AlphaFold M0R454 1-838 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564110 AgrOrtholog
BioCyc Gene G2FUF-62517 BioCyc
Ensembl Genes ENSRNOG00000047388 Ensembl
  ENSRNOG00000069644 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000069767 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044669.5 UniProtKB/TrEMBL
  ENSRNOT00000099894 ENTREZGENE
  ENSRNOT00000099894.1 UniProtKB/TrEMBL
  ENSRNOT00000110137.1 UniProtKB/TrEMBL
  ENSRNOT00000113739.1 UniProtKB/TrEMBL
Gene3D-CATH 2.10.50.30 UniProtKB/TrEMBL
  3.40.50.2300 UniProtKB/TrEMBL
InterPro ANF_lig-bd_rcpt UniProtKB/TrEMBL
  GPCR_3 UniProtKB/TrEMBL
  GPCR_3_9-Cys_dom UniProtKB/TrEMBL
  GPCR_3_9-Cys_sf UniProtKB/TrEMBL
  GPCR_3_C UniProtKB/TrEMBL
  GPCR_3_Ca_sens_rcpt-rel UniProtKB/TrEMBL
  GPCR_3_vmron_rcpt_2 UniProtKB/TrEMBL
  Peripla_BP_I UniProtKB/TrEMBL
KEGG Report rno:308248 UniProtKB/TrEMBL
NCBI Gene 308248 ENTREZGENE
PANTHER PTHR24061 UniProtKB/TrEMBL
  VOMERONASAL 2, RECEPTOR 10-RELATED UniProtKB/TrEMBL
Pfam 7tm_3 UniProtKB/TrEMBL
  ANF_receptor UniProtKB/TrEMBL
  NCD3G UniProtKB/TrEMBL
PhenoGen Vom2r4 PhenoGen
PRINTS GPCRMGR UniProtKB/TrEMBL
  VOMERONASL2R UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F3_4 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000047388 RatGTEx
  ENSRNOG00000069644 RatGTEx
  ENSRNOG00000069767 RatGTEx
Superfamily-SCOP SSF53822 UniProtKB/TrEMBL
UniProt A0A8I5ZUD7_RAT UniProtKB/TrEMBL
  A0A8I6AEC9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AFS9 ENTREZGENE, UniProtKB/TrEMBL
  D3ZF80_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Vom2r4  vomeronasal 2 receptor, 4  LOC108352192  vomeronasal type-2 receptor 116-like  Data merged from RGD:11397307 737654 PROVISIONAL
2016-08-02 LOC108352192  vomeronasal type-2 receptor 116-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-07-23 Vom2r4  vomeronasal 2 receptor, 4  RGD1564110  similar to putative pheromone receptor   Symbol and Name updated 1299863 APPROVED
2008-04-30 RGD1564110  similar to putative pheromone receptor   RGD1564110_predicted  similar to putative pheromone receptor (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564110_predicted  similar to putative pheromone receptor (predicted)  LOC308248  similar to putative pheromone receptor  Symbol and Name status set to approved 1299863 APPROVED