XLOC_012213 (vsx2)


Basic Information

Item Value
gene id XLOC_012213
gene name vsx2
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007128.7
NCBI id CM002901.2
chromosome length 53461100
location 31652640 ~ 31659670 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00024065
GGATCATGCGTATTGCGCCTCGGATGCCTGTGCACAGGGGACCGACTCGAAAGCAAAGAAGGGAATAGTCTCAGAGGCacaatgacaggaaaggatgggGCTGTTTTGTCGGAAAGTTTGAACAAATCAAAATCGCTGTGTGCCACCGAGAACGGGGGAAATAACAATCCACATCTGTCAAAGAGCAGCATCACACATCCGCCAAAATGCACGGGTTTCGGCATTCAGGAGATCTTGGGACTAAATAAAGAGCCGTCCTCGGCCCCACGGAGCACACTGGACTCCTTCCCCGCCGGGGCGCACCTTCTGGCCAGCAGGTCGATGCTCGGTCCGGCTGGTGTCGGTGTTGGGGTCGGGATGGGATTAATTGGGCCTGGAGGTATTCCGTCTTTCTACAGTCAGCCCGCGTTTCTGGAGGTTCTGTCAGACGCGCAGAACGTGCACCTCCAGCCGCTCAGCAGGACGGTGGGGCCGCTGGAACATAACCAGTCTGCCAGCTCAGATTCAGATGATGTCTCTTCAAGTGAAAGGAAAATGTCAAAGTCTTCACTGAGCCAGAGCAAGAAGAGAAAAAAGAGACGACACAGaacAATATTTACATCTTACCAGCTGGAAGAACTGGAGAAAGCTTTTAACGAGGCTCATTATCCGGATGTGTACGCCAGAGAAATGCTGGCCATGAAAACCGAGCTGCCGGAGGACAGAATACAGGTGTGGTTTCAAAACCGGAGGGCCAAGTGGAGGAAGCGGGAGAAGTGTTGGGGTCGCAGTAGCGTGATGGCGGAATACGGGCTCTACGGCGCCATGGTGCGTCACTCTATCCCTCTGCCCGAGTCTATACTCAAATCTGCTAAAGATGGCATCATGGACTCCTGTGCCCCCTGGCTTCTAGGGATGCACAAGAAGTCCTTGGAGACGGCTGGGCACCAATCAAACGAGAAGTCAGATGTCACTCAGACACCGACCAATCCCAAACCGGACGAGGCCGAGGCTGAGGAAAGGAGGACAGAGTCACCAATGTCCAAAGAGGAACTGAGGGAGAACAGCATTGCTGCTCTCAGGGCAAAAGCGCAGGAGCACAGCGCCAAAGTGCTTGGAACAGTTTCCTCAGAGAGACTAGAGCATAACATGGAGACAACGGTGACAGAGGAGAAGTCCAGCGAACAGATAGACGCAAAAGAAGAGGAAAAGAGCTCTTAGATCTTGCACTGTAACAGCATAAAGCGTAGAAAATGTCTGGGCTGTTTTCTCATCCTCAACACTGGacttttaattcttcactttagCAGGTCAGCAGCATTTAGAAATGTACAGTATTTTGATAGTAGCATTGGTTCATCCATGCAACAGGTTGATAGCCTTTTTTAAACAGAGGCCTACAAAAATCTCAGCCATAACTTCTTTTTAAGATCCTAGTTTTCAGTCACTTTTGTTATGAGCCATGTATAGATCATCATTTAAATGAAGAATTAGAAATGTATGAGACTGAACAACATTTGTTTTGAGCATCTGAGATTGAGTTACAGCAGCTGCTTCAGTATTTCAATCACTTAAAAACACTTGACTTGGGCTTGTGCGTTAAAGACAGTTATATTaatagatttaatttaatatatacacCTTACTCAATAAAACCACAAAGCACATTGTAATAAGCCATTCTATTCCATTCTAAGCCAGTTCTATTAGGTTTttccctaaaatgaaaatgtactcagcA

Function

symbol description
vsx2 Enables sequence-specific DNA binding activity. Acts upstream of or within negative regulation of transcription by RNA polymerase II and regulation of neural retina development. Predicted to be active in nucleus. Is expressed in nervous system; neural tube; optic cup; and optic vesicle. Human ortholog(s) of this gene implicated in blindness and isolated microphthalmia 2. Orthologous to human VSX2 (visual system homeobox 2).

GO:

id name namespace
GO:0050896 response to stimulus biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0007275 multicellular organism development biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0007601 visual perception biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0061074 regulation of neural retina development biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003677 DNA binding molecular_function

KEGG:

id description
ko03000 Transcription factors

ZFIN:

id description
ZDB-GENE-001222-1 Enables sequence-specific DNA binding activity. Acts upstream of or within negative regulation of transcription by RNA polymerase II and regulation of neural retina development. Predicted to be active in nucleus. Is expressed in nervous system; neural tube; optic cup; and optic vesicle. Human ortholog(s) of this gene implicated in blindness and isolated microphthalmia 2. Orthologous to human VSX2 (visual system homeobox 2).

Ensembl:

ensembl_id ENSDARG00000005574

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00024065 True 1720 mRNA 0.47 5 31652640 31659670

Neighbor

gene id symbol gene type direction distance location
XLOC_012212 znf839 coding downstream 12795 31623356 ~ 31639845 (-)
XLOC_012211 si:dkey-170l10.1 coding downstream 40948 31606635 ~ 31611692 (-)
XLOC_012210 rpap1 coding downstream 72907 31535764 ~ 31579733 (-)
XLOC_012209 ltk coding downstream 169171 31400584 ~ 31483469 (-)
XLOC_012208 BX539317.1 coding downstream 268092 31384434 ~ 31384548 (-)
XLOC_012214 lin52 coding upstream 7955 31667625 ~ 31695257 (-)
XLOC_012215 pomt2 coding upstream 36987 31696657 ~ 31712041 (-)
XLOC_012216 dtd2 coding upstream 57522 31717192 ~ 31719071 (-)
XLOC_012217 abraxas2 coding upstream 146105 31805775 ~ 31819837 (-)
XLOC_012218 NA coding upstream 468227 32127897 ~ 32136128 (-)
XLOC_012203 BX571712.2 non-coding downstream 467397 31181950 ~ 31185243 (-)
XLOC_012201 BX571712.1 non-coding downstream 555099 31096326 ~ 31097541 (-)
XLOC_012193 NA non-coding downstream 1059582 30573572 ~ 30593058 (-)
XLOC_012190 NA non-coding downstream 1242881 30398949 ~ 30409759 (-)
XLOC_012219 CR407546.1 non-coding upstream 586459 32246129 ~ 32246255 (-)
XLOC_012228 NA non-coding upstream 1474149 33133819 ~ 33138376 (-)
XLOC_012229 NA non-coding upstream 1485924 33145594 ~ 33162478 (-)
XLOC_012230 AL590149.1 non-coding upstream 1547110 33206780 ~ 33231714 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000189_03517928_03524647 VSX2 coding CI01000189 null 3517283 ~ 3524712 (-)
bowfin (Amia calva) AMCG00000416 LOC106608304 coding CM030141.1 CM030141.1 14316161 ~ 14340047 (+)