Vsig4 (V-set and immunoglobulin domain containing 4) - Rat Genome Database

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Gene: Vsig4 (V-set and immunoglobulin domain containing 4) Rattus norvegicus
Analyze
Symbol: Vsig4
Name: V-set and immunoglobulin domain containing 4
RGD ID: 1564659
Description: Predicted to enable complement component C3b binding activity. Involved in positive regulation of gene expression. Predicted to be located in membrane. Predicted to be part of protein-containing complex. Orthologous to human VSIG4 (V-set and immunoglobulin domain containing 4); INTERACTS WITH 3-chloropropane-1,2-diol; acetamide; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC312102; LOC312102; MGC108984; V-set and immunoglobulin domain-containing protein 4
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
GRCr8X65,154,422 - 65,179,708 (-)NCBIGRCr8
mRatBN7.2X61,144,926 - 61,170,212 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX61,144,928 - 61,170,212 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX62,618,577 - 62,643,869 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X66,119,103 - 66,144,391 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X63,676,350 - 63,701,634 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X65,370,851 - 65,400,298 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX65,370,851 - 65,400,298 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X66,208,997 - 66,234,590 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X83,872,092 - 83,898,242 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX61,557,850 - 61,582,973 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Transcriptomic Analysis of Rat Macrophages. Pridans C, etal., Front Immunol. 2021 Feb 1;11:594594. doi: 10.3389/fimmu.2020.594594. eCollection 2020.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. 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:17016562   PMID:17051150   PMID:23376485  


Genomics

Comparative Map Data
Vsig4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X65,154,422 - 65,179,708 (-)NCBIGRCr8
mRatBN7.2X61,144,926 - 61,170,212 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX61,144,928 - 61,170,212 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX62,618,577 - 62,643,869 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X66,119,103 - 66,144,391 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X63,676,350 - 63,701,634 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X65,370,851 - 65,400,298 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX65,370,851 - 65,400,298 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X66,208,997 - 66,234,590 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X83,872,092 - 83,898,242 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX61,557,850 - 61,582,973 (-)NCBICelera
Cytogenetic MapXq22NCBI
VSIG4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X66,021,738 - 66,040,080 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX66,021,738 - 66,040,125 (-)EnsemblGRCh38hg38GRCh38
GRCh37X65,241,580 - 65,259,922 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X65,158,305 - 65,176,692 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X65,024,600 - 65,042,906NCBI
CeleraX65,588,725 - 65,607,111 (-)NCBICelera
Cytogenetic MapXq12NCBI
HuRefX59,068,686 - 59,087,663 (-)NCBIHuRef
CHM1_1X65,134,610 - 65,152,555 (-)NCBICHM1_1
T2T-CHM13v2.0X64,448,234 - 64,467,291 (-)NCBIT2T-CHM13v2.0
Vsig4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X95,290,807 - 95,337,044 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX95,290,809 - 95,337,044 (-)EnsemblGRCm39 Ensembl
GRCm38X96,247,201 - 96,293,438 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX96,247,203 - 96,293,438 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X93,442,542 - 93,488,777 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X92,449,922 - 92,496,157 (-)NCBIMGSCv36mm8
CeleraX83,251,817 - 83,298,808 (-)NCBICelera
Cytogenetic MapXC3NCBI
cM MapX42.69NCBI
Vsig4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554755,461,064 - 5,481,564 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554755,461,512 - 5,481,552 (-)NCBIChiLan1.0ChiLan1.0
VSIG4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X65,546,150 - 65,563,779 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X65,549,755 - 65,567,384 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X55,137,938 - 55,155,569 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X65,211,313 - 65,228,888 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX65,211,313 - 65,229,332 (-)Ensemblpanpan1.1panPan2
VSIG4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X50,839,979 - 50,881,684 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX50,803,330 - 50,881,618 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX41,659,551 - 41,719,546 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X51,785,928 - 51,845,934 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX51,806,749 - 51,845,903 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X49,750,420 - 49,810,399 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X51,098,349 - 51,158,343 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X51,013,686 - 51,073,693 (-)NCBIUU_Cfam_GSD_1.0
Vsig4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X51,402,029 - 51,426,149 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366352,167,617 - 2,191,740 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366352,167,633 - 2,191,725 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VSIG4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX52,175,607 - 52,198,566 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X52,175,601 - 52,198,635 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X58,745,331 - 58,775,852 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VSIG4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X55,963,007 - 55,982,929 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX55,962,866 - 55,981,287 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660833,291,053 - 3,309,343 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vsig4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248981,268,886 - 1,289,180 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248981,268,998 - 1,288,756 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vsig4
61 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:44
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000032121
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X5704214165612192Rat


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 21 21 21 1
Low 10 19 8 15 8 3 3 2 5 10 3
Below cutoff 1 13 8 4 3 4 5 5 9 7 9 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000032121   ⟹   ENSRNOP00000036992
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX61,144,928 - 61,170,212 (-)Ensembl
Rnor_6.0 EnsemblX65,370,851 - 65,400,298 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100120   ⟹   ENSRNOP00000092739
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX61,145,441 - 61,167,846 (-)Ensembl
RefSeq Acc Id: NM_001025004   ⟹   NP_001020175
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X65,154,422 - 65,179,708 (-)NCBI
mRatBN7.2X61,144,926 - 61,170,212 (-)NCBI
Rnor_6.0X65,370,851 - 65,400,298 (-)NCBI
Rnor_5.0X66,208,997 - 66,234,590 (-)NCBI
RGSC_v3.4X83,872,092 - 83,898,242 (-)RGD
CeleraX61,557,850 - 61,582,973 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001020175 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91234 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000036992
  ENSRNOP00000036992.4
  ENSRNOP00000092739.1
Reference Protein Sequences
RefSeq Acc Id: NP_001020175   ⟸   NM_001025004
- Peptide Label: precursor
- UniProtKB: F7FEU1 (UniProtKB/TrEMBL),   A0A8I6AIJ0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000036992   ⟸   ENSRNOT00000032121
RefSeq Acc Id: ENSRNOP00000092739   ⟸   ENSRNOT00000100120
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F7FEU1-F1-model_v2 AlphaFold F7FEU1 1-285 view protein structure

Transcriptome

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

Promoters
RGD ID:13701853
Promoter ID:EPDNEW_R12376
Type:single initiation site
Name:Vsig4_1
Description:V-set and immunoglobulin 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_6.0X65,400,315 - 65,400,375EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564659 AgrOrtholog
BioCyc Gene G2FUF-2185 BioCyc
Ensembl Genes ENSRNOG00000038132 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000032121 ENTREZGENE
  ENSRNOT00000032121.6 UniProtKB/TrEMBL
  ENSRNOT00000100120.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7322659 IMAGE-MGC_LOAD
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  VSIG4 UniProtKB/TrEMBL
KEGG Report rno:312102 UniProtKB/TrEMBL
MGC_CLONE MGC:108984 IMAGE-MGC_LOAD
NCBI Gene 312102 ENTREZGENE
PANTHER PTHR15466 UniProtKB/TrEMBL
  V-SET AND IMMUNOGLOBULIN DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
Pfam V-set UniProtKB/TrEMBL
PhenoGen Vsig4 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000038132 RatGTEx
SMART IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A8I6AIJ0 ENTREZGENE, UniProtKB/TrEMBL
  F7FEU1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Vsig4  V-set and immunoglobulin domain containing 4  LOC312102  hypothetical protein LOC312102  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC312102  hypothetical protein LOC312102      Symbol and Name status set to provisional 70820 PROVISIONAL