Vxn (vexin) - Rat Genome Database

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Gene: Vxn (vexin) Rattus norvegicus
Analyze
Symbol: Vxn
Name: vexin
RGD ID: 1561849
Description: Predicted to be involved in neuron differentiation. Predicted to be located in nucleus and plasma membrane. Orthologous to human VXN (vexin); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC500393; LOC500393; RGD1561849; similar to RIKEN cDNA 3110035E14; uncharacterized protein C8orf46 homolog; uncharacterized protein LOC500393
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
GRCr8514,442,040 - 14,467,500 (-)NCBIGRCr8
mRatBN7.259,659,213 - 9,684,684 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl59,659,213 - 9,684,684 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx511,813,006 - 11,838,372 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0513,444,516 - 13,469,930 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0513,147,685 - 13,173,047 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.059,355,490 - 9,381,161 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl59,355,507 - 9,381,214 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0514,155,561 - 14,181,247 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.459,213,351 - 9,238,896 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera59,168,425 - 9,193,809 (-)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (ISO)
plasma membrane  (ISO)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:29518376  


Genomics

Comparative Map Data
Vxn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8514,442,040 - 14,467,500 (-)NCBIGRCr8
mRatBN7.259,659,213 - 9,684,684 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl59,659,213 - 9,684,684 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx511,813,006 - 11,838,372 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0513,444,516 - 13,469,930 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0513,147,685 - 13,173,047 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.059,355,490 - 9,381,161 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl59,355,507 - 9,381,214 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0514,155,561 - 14,181,247 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.459,213,351 - 9,238,896 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera59,168,425 - 9,193,809 (-)NCBICelera
Cytogenetic Map5q11NCBI
VXN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38866,493,566 - 66,518,524 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl866,492,326 - 66,518,524 (+)EnsemblGRCh38hg38GRCh38
GRCh37867,405,801 - 67,430,759 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36867,568,321 - 67,593,294 (+)NCBINCBI36Build 36hg18NCBI36
Celera863,398,468 - 63,423,736 (+)NCBICelera
Cytogenetic Map8q13.1NCBI
HuRef862,895,478 - 62,920,746 (+)NCBIHuRef
CHM1_1867,460,384 - 67,485,645 (+)NCBICHM1_1
T2T-CHM13v2.0866,919,332 - 66,944,291 (+)NCBIT2T-CHM13v2.0
Vxn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3919,671,492 - 9,697,367 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl19,671,424 - 9,697,368 (+)EnsemblGRCm39 Ensembl
GRCm3819,601,267 - 9,627,142 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl19,601,199 - 9,627,143 (+)EnsemblGRCm38mm10GRCm38
MGSCv3719,591,348 - 9,617,223 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3619,586,481 - 9,612,356 (+)NCBIMGSCv36mm8
Celera19,575,385 - 9,601,183 (+)NCBICelera
Cytogenetic Map1A2NCBI
cM Map12.08NCBI
Vxn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544412,659,776 - 12,685,055 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544412,659,894 - 12,684,919 (-)NCBIChiLan1.0ChiLan1.0
VXN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2782,230,778 - 82,256,299 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1857,870,155 - 57,895,686 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0863,036,312 - 63,061,857 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1864,702,663 - 64,728,092 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl864,702,663 - 64,728,092 (+)Ensemblpanpan1.1panPan2
VXN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12916,078,154 - 16,101,873 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2916,078,658 - 16,099,606 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2916,394,538 - 16,418,123 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02916,158,801 - 16,182,388 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2916,097,773 - 16,182,387 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12916,190,634 - 16,214,160 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02916,290,258 - 16,313,838 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02916,546,239 - 16,569,616 (+)NCBIUU_Cfam_GSD_1.0
Vxn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530367,277,747 - 67,301,812 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364967,483,679 - 7,507,756 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364967,483,685 - 7,529,094 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VXN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl468,202,216 - 68,224,811 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1468,202,216 - 68,225,131 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2474,369,674 - 74,392,420 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VXN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1862,367,420 - 62,395,326 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl862,367,667 - 62,395,286 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603979,112,419 - 79,140,096 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vxn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474424,835,784 - 24,858,989 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474424,835,705 - 24,858,988 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vxn
172 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:761
Count of miRNA genes:305
Interacting mature miRNAs:400
Transcripts:ENSRNOT00000039237
Prediction methods:Microtar, Miranda, 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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat

Markers in Region
RH130324  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.259,659,263 - 9,659,470 (+)MAPPERmRatBN7.2
Rnor_6.059,355,541 - 9,355,747NCBIRnor6.0
Rnor_5.0514,155,612 - 14,155,818UniSTSRnor5.0
RGSC_v3.459,213,402 - 9,213,608UniSTSRGSC3.4
Celera59,168,476 - 9,168,682UniSTS
Cytogenetic Map5q11UniSTS


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 46 7
Low 2 15 31 15 18 15 8 9 28 21 34 11 8
Below cutoff 1 18 24 24 1 24 2 14

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039237   ⟹   ENSRNOP00000032720
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl59,659,213 - 9,684,684 (-)Ensembl
Rnor_6.0 Ensembl59,355,507 - 9,381,214 (-)Ensembl
RefSeq Acc Id: NM_001109260   ⟹   NP_001102730
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8514,442,040 - 14,467,500 (-)NCBI
mRatBN7.259,659,213 - 9,684,684 (-)NCBI
Rnor_6.059,355,490 - 9,381,161 (-)NCBI
Rnor_5.0514,155,561 - 14,181,247 (-)NCBI
RGSC_v3.459,213,351 - 9,238,896 (-)RGD
Celera59,168,425 - 9,193,809 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102730 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11560 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000032720
  ENSRNOP00000032720.3
Reference Protein Sequences
RefSeq Acc Id: NP_001102730   ⟸   NM_001109260
- UniProtKB: D3ZVT4 (UniProtKB/TrEMBL),   A6JFG3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000032720   ⟸   ENSRNOT00000039237
Protein Domains
Vexin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZVT4-F1-model_v2 AlphaFold D3ZVT4 1-207 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:1561849 AgrOrtholog
BioCyc Gene G2FUF-42196 BioCyc
Ensembl Genes ENSRNOG00000021663 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039237 ENTREZGENE
  ENSRNOT00000039237.5 UniProtKB/TrEMBL
InterPro DUF4648 UniProtKB/TrEMBL
  Vexin UniProtKB/TrEMBL
KEGG Report rno:500393 UniProtKB/TrEMBL
NCBI Gene 500393 ENTREZGENE
PANTHER PTHR31520 UniProtKB/TrEMBL
  VEXIN UniProtKB/TrEMBL
Pfam DUF4648 UniProtKB/TrEMBL
PhenoGen Vxn PhenoGen
RatGTEx ENSRNOG00000021663 RatGTEx
UniProt A6JFG3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZVT4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-04 Vxn  vexin  RGD1561849  similar to RIKEN cDNA 3110035E14  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1561849  similar to RIKEN cDNA 3110035E14   RGD1561849_predicted  similar to RIKEN cDNA 3110035E14 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1561849_predicted  similar to RIKEN cDNA 3110035E14 (predicted)  LOC500393  similar to RIKEN cDNA 3110035E14  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500393  similar to RIKEN cDNA 3110035E14      Symbol and Name status set to provisional 70820 PROVISIONAL