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

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Advanced Search (OLGA)
Gene: Vsig4 (V-set and immunoglobulin domain containing 4) Mus musculus
Analyze
Symbol: Vsig4
Name: V-set and immunoglobulin domain containing 4
RGD ID: 1558365
MGI Page MGI
Description: Predicted to enable complement component C3b binding activity. Acts upstream of or within negative regulation of T cell proliferation and negative regulation of interleukin-2 production. Predicted to be part of protein-containing complex. Is expressed in bone marrow; oviduct; and thyroid gland. Orthologous to human VSIG4 (V-set and immunoglobulin domain containing 4).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: A530061A11; BC025105; complement receptor of the immunoglobulin superfamily; CR; CRIg; MGC36211; V-set and immunoglobulin domain-containing protein 4; Z39I; Z39IG
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal cholesterol homeostasis  (IEA)
abnormal enterocyte proliferation  (IAGP)
abnormal macrophage physiology  (IAGP)
abnormal platelet physiology  (IAGP)
abnormal sleep behavior  (IEA)
decreased circulating glucose level  (IEA)
decreased locomotor activity  (IEA)
decreased lymphocyte cell number  (IAGP)
decreased mean corpuscular hemoglobin  (IEA)
decreased susceptibility to experimental autoimmune encephalomyelitis  (IAGP)
decreased susceptibility to induced colitis  (IAGP)
decreased T helper 1 cell number  (IAGP)
decreased T-helper 17 cell number  (IAGP)
decreased total body fat amount  (IEA)
hyperactivity  (IEA)
increased blood urea nitrogen level  (IEA)
increased circulating alanine transaminase level  (IEA)
increased circulating alkaline phosphatase level  (IEA)
increased circulating aspartate transaminase level  (IEA)
increased circulating interleukin-1 beta level  (IAGP)
increased circulating potassium level  (IEA)
increased circulating sodium level  (IEA)
increased heart weight  (IEA)
increased interleukin-1 beta secretion  (IAGP)
increased lean body mass  (IEA)
increased susceptibility to bacterial infection  (IAGP)
increased susceptibility to experimental autoimmune encephalomyelitis  (IAGP)
increased susceptibility to induced colitis  (IAGP)
increased susceptibility to induced morbidity/mortality  (IAGP)
increased T-helper 1 cell number  (IAGP)
increased T-helper 17 cell number  (IAGP)
increased urine microalbumin level  (IEA)
increased vertical activity  (IEA)
References

References - curated
# Reference Title Reference Citation
1. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
2. Mouse MP Annotation Import Pipeline RGD automated import pipeline
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:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:16141072   PMID:16141073   PMID:16530040   PMID:17016562   PMID:17548523   PMID:18524992   PMID:19017980   PMID:19136662  
PMID:20487640   PMID:21677750   PMID:21768202   PMID:21873635   PMID:23225913   PMID:23280470   PMID:24194600   PMID:24424721   PMID:24862966   PMID:25114177   PMID:25929804   PMID:27345697  
PMID:27440002   PMID:29109438   PMID:29171836   PMID:29235119   PMID:29268030   PMID:30662948   PMID:31266632   PMID:31594939   PMID:31723045   PMID:31784084   PMID:32856419   PMID:34023853  
PMID:34887405   PMID:35013905   PMID:35258552   PMID:36063598   PMID:36103821   PMID:36440192   PMID:36821387   PMID:37153746   PMID:37520546   PMID:38355793   PMID:38759519  


Genomics

Comparative Map Data
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
(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
(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
(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
982 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:238
Count of miRNA genes:204
Interacting mature miRNAs:215
Transcripts:ENSMUST00000050707, ENSMUST00000146830
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4141630Gct6_mgranulosa cell tumorigenesis 6 (mouse)Not determined47179121129764756Mouse
13208552Wght12_mweight 12 (mouse)X94043606149782996Mouse
4141803Lmr30_mleishmaniasis resistance 30 (mouse)Not determined85062606119062720Mouse
1302054Gct4_mgranulosa cell tumorigenesis 4 (mouse)Not determinedX76124336102062720Mouse
13208556Lgth14_mbody length 14 (mouse)X94043606149782996Mouse
13824980Ferq1_mgenetic fertility QTL 1 (mouse)X54045360148782996Mouse
11075102Modc2_mmodifier of Odc2 (mouse)X80189914114190059Mouse
1357500Mdmsc6_mmodifier of muscularity 6 (mouse)Not determinedX75306671109306758Mouse
12879918Shm4_msperm head morphology 4 (mouse)X72072050102062720Mouse
25314318Sccor2_msynaptonemal complex length to mean MLH1 count ratio 2 (mouse)X7054360696543606Mouse
1357433Dbts2_mdiabetes 2 (mouse)Not determinedX7226295150107038Mouse
4141665Mhysq2_mmale hybrid sterility QTL 2 (mouse)Not determined71453852139203212Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000050707   ⟹   ENSMUSP00000051521
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 EnsemblX95,290,809 - 95,337,044 (-)Ensembl
GRCm38.p6 EnsemblX96,247,203 - 96,293,438 (-)Ensembl
Ensembl Acc Id: ENSMUST00000146830
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 EnsemblX95,293,556 - 95,337,018 (-)Ensembl
GRCm38.p6 EnsemblX96,249,950 - 96,293,412 (-)Ensembl
RefSeq Acc Id: NM_177789   ⟹   NP_808457
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39X95,290,807 - 95,337,044 (-)NCBI
GRCm38X96,247,201 - 96,293,438 (-)NCBI
MGSCv37X93,442,542 - 93,488,777 (-)RGD
CeleraX83,251,817 - 83,298,808 (-)RGD
cM MapX ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_808457 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH25105 (Get FASTA)   NCBI Sequence Viewer  
  BAC30780 (Get FASTA)   NCBI Sequence Viewer  
  CAG24385 (Get FASTA)   NCBI Sequence Viewer  
  CAV28322 (Get FASTA)   NCBI Sequence Viewer  
  EDL14218 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000051521
  ENSMUSP00000051521.2
RefSeq Acc Id: NP_808457   ⟸   NM_177789
- Peptide Label: precursor
- UniProtKB: F6TUL9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000051521   ⟸   ENSMUST00000050707
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F6TUL9-F1-model_v2 AlphaFold F6TUL9 1-280 view protein structure

Promoters
RGD ID:13680984
Promoter ID:EPDNEW_M24641
Type:multiple initiation site
Name:Vsig4_1
Description:Mus musculus V-set and immunoglobulin domain containing 4 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38X96,293,438 - 96,293,498EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2679720 AgrOrtholog
Ensembl Genes ENSMUSG00000044206 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000050707 ENTREZGENE
  ENSMUST00000050707.3 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
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 mmu:278180 UniProtKB/TrEMBL
MGD MGI:2679720 ENTREZGENE
NCBI Gene 278180 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
SMART SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt F6TUL9 ENTREZGENE, UniProtKB/TrEMBL