Vcsa2 (variable coding sequence A2) - Rat Genome Database

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Gene: Vcsa2 (variable coding sequence A2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Vcsa2
Name: variable coding sequence A2
RGD ID: 3954
Description: Predicted to enable endopeptidase inhibitor activity. Predicted to be involved in regulation of sensory perception of pain. Predicted to be located in extracellular region. Orthologous to human SMR3B (submaxillary gland androgen regulated protein 3B); INTERACTS WITH ammonium chloride; methamphetamine; trichloroethene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: SMR1-alpha2; VCS-alpha2
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,127,218 - 20,133,683 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1420,127,218 - 20,133,683 (-)EnsemblGRCr8
mRatBN7.21419,851,232 - 19,857,697 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1419,851,232 - 19,857,697 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1419,808,644 - 19,815,126 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,127,523 - 21,134,007 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01419,852,890 - 19,859,367 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,558,489 - 21,564,115 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,558,489 - 21,615,488 (-)Ensemblrn6Rnor6.0
Rnor_5.01421,466,929 - 21,472,555 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41421,438,442 - 21,444,907 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1419,176,400 - 19,182,865 (-)NCBICelera
RGSC_v3.11421,438,441 - 21,444,907 (-)NCBI
Cytogenetic Map14p22NCBI
JBrowse:




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

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Episodic evolution and rapid divergence of members of the rat multigene family encoding the salivary prohormone-like protein SMR1. Courty Y, etal., Mol Biol Evol 1996 Jul;13(6):758-66.
2. 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.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Vcsa2
43 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:19
Count of miRNA genes:19
Interacting mature miRNAs:19
Transcripts:ENSRNOT00000002667
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14395787821572472Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141787564536079022Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14140068101Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14140068101Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14939329839411170Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141133490630674469Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141133471628389666Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14395787831121464Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14862139853621398Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141891545442433608Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14395787824886169Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141889519263895192Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141790672654251504Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141415516Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14131893212Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14862139853621398Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141513759431238250Rat

Markers in Region
D14Wox13  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21419,848,039 - 19,848,270 (+)MAPPERmRatBN7.2
mRatBN7.21419,858,811 - 19,859,012 (+)MAPPERmRatBN7.2
Rnor_6.01421,555,076 - 21,555,306NCBIRnor6.0
Rnor_6.01421,565,227 - 21,565,427NCBIRnor6.0
Rnor_5.01421,473,667 - 21,473,867UniSTSRnor5.0
Rnor_5.01421,463,516 - 21,463,746UniSTSRnor5.0
RGSC_v3.41421,435,249 - 21,435,480RGDRGSC3.4
RGSC_v3.41421,383,854 - 21,384,062RGDRGSC3.4
RGSC_v3.41421,446,021 - 21,446,222RGDRGSC3.4
RGSC_v3.11421,435,249 - 21,435,480RGD
RH 3.4 Map14288.2RGD
RH 3.4 Map14288.2UniSTS
Cytogenetic Map14p22-p21UniSTS
D14Wox17  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21419,858,792 - 19,859,003 (+)MAPPERmRatBN7.2
Rnor_6.01421,565,208 - 21,565,418NCBIRnor6.0
Rnor_5.01421,473,648 - 21,473,858UniSTSRnor5.0
RGSC_v3.41421,446,003 - 21,446,213UniSTSRGSC3.4
RGSC_v3.41421,383,836 - 21,384,053UniSTSRGSC3.4
Celera1419,122,968 - 19,123,179UniSTS
Celera1419,183,961 - 19,184,171UniSTS
Cytogenetic Map14p22-p21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
3 2 1 18 17 21 3 25 3 47 33 11 6 25 18

Sequence


Ensembl Acc Id: ENSRNOT00000002667   ⟹   ENSRNOP00000002667
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1420,127,218 - 20,133,683 (-)Ensembl
mRatBN7.2 Ensembl1419,851,232 - 19,857,697 (-)Ensembl
Rnor_6.0 Ensembl1421,558,489 - 21,615,488 (-)Ensembl
RefSeq Acc Id: NM_198729   ⟹   NP_942024
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81420,127,218 - 20,133,683 (-)NCBI
mRatBN7.21419,851,232 - 19,857,697 (-)NCBI
Rnor_6.01421,558,489 - 21,564,115 (-)NCBI
Rnor_5.01421,466,929 - 21,472,555 (-)NCBI
RGSC_v3.41421,438,442 - 21,444,907 (-)RGD
Celera1419,176,400 - 19,182,865 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_942024 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA54830 (Get FASTA)   NCBI Sequence Viewer  
  CAA54832 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002667
  ENSRNOP00000002667.5
RefSeq Acc Id: NP_942024   ⟸   NM_198729
- Peptide Label: precursor
- UniProtKB: A6KKK4 (UniProtKB/TrEMBL),   G3V685 (UniProtKB/TrEMBL),   P70676 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000002667   ⟸   ENSRNOT00000002667

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V685-F1-model_v2 AlphaFold G3V685 1-115 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:3954 AgrOrtholog
BioCyc Gene G2FUF-16150 BioCyc
Ensembl Genes ENSRNOG00000001945 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002667 ENTREZGENE
  ENSRNOT00000002667.7 UniProtKB/TrEMBL
InterPro SMR UniProtKB/TrEMBL
KEGG Report rno:289526 UniProtKB/TrEMBL
NCBI Gene Vcsa2 ENTREZGENE
PANTHER PTHR14179 UniProtKB/TrEMBL
  SUBMAXILLARY GLAND ANDROGEN REGULATED PROTEIN 2 LIKE-RELATED UniProtKB/TrEMBL
Pfam PROL5-SMR UniProtKB/TrEMBL
PhenoGen Vcsa2 PhenoGen
PROSITE PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001945 RatGTEx
UniProt A6KKK4 ENTREZGENE, UniProtKB/TrEMBL
  G3V685 ENTREZGENE, UniProtKB/TrEMBL
  P70676 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Vcsa2  Variable coding sequence A2      Symbol and Name status set to approved 70586 APPROVED