Vsx2 (visual system homeobox 2) - Rat Genome Database

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Gene: Vsx2 (visual system homeobox 2) Rattus norvegicus
Analyze
Symbol: Vsx2
Name: visual system homeobox 2
RGD ID: 621215
Description: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including negative regulation of neuroblast proliferation; neuron differentiation; and positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in blindness and isolated microphthalmia 2. Orthologous to human VSX2 (visual system homeobox 2); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C. elegans ceh-10 homeo domain containing homolog; ceh-10 homeo domain containing homolog; ceh-10 homeo domain containing homolog (C. elegans); Chx10
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86109,932,943 - 109,972,005 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl6109,948,313 - 109,971,100 (+)EnsemblGRCr8
mRatBN7.26104,214,842 - 104,240,264 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6104,217,230 - 104,240,018 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx6104,379,571 - 104,402,356 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06104,678,655 - 104,701,440 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06104,048,242 - 104,071,028 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.06108,285,031 - 108,308,588 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,285,822 - 108,308,587 (+)Ensemblrn6Rnor6.0
Rnor_5.06117,237,657 - 117,260,423 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.46108,638,063 - 108,660,830 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera6102,045,137 - 102,067,982 (+)NCBICelera
RGSC_v3.16108,647,664 - 108,647,779 (+)NCBI
Cytogenetic Map6q31NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Human microphthalmia associated with mutations in the retinal homeobox gene CHX10. Ferda Percin E, etal., Nat Genet 2000 Aug;25(4):397-401.
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8630490   PMID:10482234   PMID:15576400   PMID:15767664   PMID:16236706   PMID:16384989   PMID:16547132   PMID:16854970   PMID:19389377  


Genomics

Comparative Map Data
Vsx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86109,932,943 - 109,972,005 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl6109,948,313 - 109,971,100 (+)EnsemblGRCr8
mRatBN7.26104,214,842 - 104,240,264 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6104,217,230 - 104,240,018 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx6104,379,571 - 104,402,356 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06104,678,655 - 104,701,440 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06104,048,242 - 104,071,028 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.06108,285,031 - 108,308,588 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,285,822 - 108,308,587 (+)Ensemblrn6Rnor6.0
Rnor_5.06117,237,657 - 117,260,423 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.46108,638,063 - 108,660,830 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera6102,045,137 - 102,067,982 (+)NCBICelera
RGSC_v3.16108,647,664 - 108,647,779 (+)NCBI
Cytogenetic Map6q31NCBI
VSX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381474,239,449 - 74,262,738 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1474,239,449 - 74,262,738 (+)Ensemblhg38GRCh38
GRCh371474,706,152 - 74,729,441 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361473,775,928 - 73,799,194 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341473,775,927 - 73,799,193NCBI
Celera1454,743,463 - 54,766,749 (+)NCBICelera
Cytogenetic Map14q24.3NCBI
HuRef1454,873,146 - 54,896,407 (+)NCBIHuRef
CHM1_11474,645,738 - 74,668,970 (+)NCBICHM1_1
T2T-CHM13v2.01468,447,256 - 68,470,582 (+)NCBIT2T-CHM13v2.0
Vsx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391284,616,602 - 84,642,231 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1284,616,536 - 84,642,231 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381284,569,828 - 84,595,457 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1284,569,762 - 84,595,457 (+)Ensemblmm10GRCm38
MGSCv371285,910,802 - 85,936,407 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361285,459,600 - 85,485,205 (+)NCBIMGSCv36mm8
Celera1286,025,411 - 86,051,063 (+)NCBICelera
Cytogenetic Map12D1NCBI
cM Map1239.28NCBI
Vsx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555231,193,686 - 1,210,641 (-)Ensembl
ChiLan1.0NW_0049555231,192,035 - 1,207,949 (-)NCBIChiLan1.0ChiLan1.0
VSX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21575,328,455 - 75,349,803 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11474,544,961 - 74,566,309 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01454,797,734 - 54,821,081 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11473,651,133 - 73,672,666 (+)NCBIPanPan1.1PanPan1.1panPan2
VSX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1847,455,337 - 47,473,786 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl847,455,340 - 47,473,684 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha847,140,385 - 47,158,661 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0847,682,709 - 47,700,996 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl847,682,709 - 47,700,979 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1847,351,896 - 47,370,154 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0847,373,742 - 47,392,004 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0847,760,454 - 47,778,742 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Vsx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864028,561,166 - 28,581,265 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364883,487,702 - 3,508,191 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364883,487,718 - 3,507,802 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VSX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl797,531,860 - 97,552,033 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1797,532,021 - 97,551,072 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27103,375,425 - 103,394,310 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VSX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12451,446,781 - 51,471,156 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2451,447,714 - 51,469,345 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605339,680,858 - 39,704,250 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vsx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473427,344,221 - 27,363,372 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473427,342,668 - 27,363,372 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Vsx2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1798,679,130 - 98,702,717 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vsx2
166 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:625
Count of miRNA genes:271
Interacting mature miRNAs:335
Transcripts:ENSRNOT00000015889
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293088Iddm28Insulin dependent diabetes mellitus QTL 285.21blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)668767270135411972Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)688019181136741135Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6106095977147156653Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)684490437129490437Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6101593607138161926Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)699437079125323237Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)686494122112380234Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)699708426112483760Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)671278722116278722Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)693560258136550638Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)690871046135871046Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)698944780143944780Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)6100704576136029228Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)679198463144254945Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)646050607116278722Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)693778632138778632Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)620859430113082285Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)686867923110125012Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)686867923110125012Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)690871046135871046Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)693560258136550638Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)678204640123204640Rat
1581550Pur8Proteinuria QTL 8urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)693560258136550638Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)676937178121937178Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)6101593607146593607Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
10 12 62 147 77 76 45 60 45 6 286 155 11 124 68 75 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000015889   ⟹   ENSRNOP00000015889
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl6109,948,313 - 109,971,100 (+)Ensembl
mRatBN7.2 Ensembl6104,217,230 - 104,240,018 (+)Ensembl
Rnor_6.0 Ensembl6108,285,822 - 108,308,587 (+)Ensembl
RefSeq Acc Id: NM_001169128   ⟹   NP_001162599
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86109,948,313 - 109,971,100 (+)NCBI
mRatBN7.26104,217,230 - 104,240,018 (+)NCBI
Rnor_6.06108,285,798 - 108,308,585 (+)NCBI
Rnor_5.06117,237,657 - 117,260,423 (-)NCBI
RGSC_v3.46108,638,063 - 108,660,830 (+)RGD
Celera6102,045,137 - 102,067,982 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594026   ⟹   XP_017449515
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86109,932,943 - 109,972,005 (+)NCBI
mRatBN7.26104,214,842 - 104,240,264 (+)NCBI
Rnor_6.06108,285,031 - 108,308,588 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001162599 (Get FASTA)   NCBI Sequence Viewer  
  XP_017449515 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK70506 (Get FASTA)   NCBI Sequence Viewer  
  EDL81517 (Get FASTA)   NCBI Sequence Viewer  
  EDL81518 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000015889
  ENSRNOP00000015889.6
RefSeq Acc Id: NP_001162599   ⟸   NM_001169128
- UniProtKB: G3V7K0 (UniProtKB/TrEMBL),   A6JDX4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017449515   ⟸   XM_017594026
- Peptide Label: isoform X1
- UniProtKB: A6JDX3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000015889   ⟸   ENSRNOT00000015889
Protein Domains
CVC   Homeobox   OAR

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V7K0-F1-model_v2 AlphaFold G3V7K0 1-361 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:621215 AgrOrtholog
BioCyc Gene G2FUF-36816 BioCyc
Ensembl Genes ENSRNOG00000011918 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015889 ENTREZGENE
  ENSRNOT00000015889.8 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro CVC UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  OAR_dom UniProtKB/TrEMBL
  VSX_homeobox_regulators UniProtKB/TrEMBL
KEGG Report rno:171360 UniProtKB/TrEMBL
NCBI Gene 171360 ENTREZGENE
PANTHER VISUAL SYSTEM HOMEOBOX 2 UniProtKB/TrEMBL
  VISUAL SYSTEM HOMEOBOX 2 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
  OAR UniProtKB/TrEMBL
PhenoGen Vsx2 PhenoGen
PROSITE CVC UniProtKB/TrEMBL
  HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
  OAR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011918 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6JDX3 ENTREZGENE, UniProtKB/TrEMBL
  A6JDX4 ENTREZGENE, UniProtKB/TrEMBL
  G3V7K0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-19 Vsx2  visual system homeobox 2  Chx10  ceh-10 homeo domain containing homolog (C. elegans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Chx10  ceh-10 homeo domain containing homolog (C. elegans)    C. elegans ceh-10 homeo domain containing homolog  Name updated 1299863 APPROVED
2002-08-07 Chx10  C. elegans ceh-10 homeo domain containing homolog      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_other mouse homolog is mutated in the ocular retardationJ mutant 634855