LOC110527518 (vsx1)


Basic Information

Item Value
gene id LOC110527518
gene name vsx1
gene type coding
species rainbow trout (Oncorhynchus mykiss)
category of species economic fish

Chromosome Information

Item Value
chromosome id NC_048565.1
NCBI id CM023219.2
chromosome length 95772356
location 67288562 ~ 67291218 (-)
genome version USDA_OmykA_1.1_2020_rainbow_trout_Genome

Sequence

>XM_021608848.2
CCCGCCTCATCACCCCGAGCTacaggagaaagagaaagtagCGCTTTACAATGACAACCATGACAGGAAGAGATGATGGCTCGGATGAAAAGCCCAAAGTCAAGATGCTGGCTCCATCATTTGGGATCGATAAGTCACGACTTCATGGATCTGGGTTTAGGTCTAAAGGCTTTGCCATCACGGACCTACTGGGTCTTGAAACGGATCTCCAGCCTCGCCCATCCGGACCTCATGGAGTAGGAGGTAACGGGGATATTCAGAGCACTGGGATGGGATTCCCTTTCGCTGGAGGATCCTTGCCGcttggtctagggtttctgtgcAGTTTGGCGGCTCAGCAACCTGCGGGAGCCCCCTGCTTCCTACCGAGTCACATACCCCTCCTTCAGTCCAGGACCGAGAGTCATTTCATGCAGAACTTGGAGCAACAAAGAGACCCCTACTCTGATGATGAATGTCTCTCTGGTGATCGAAACGATTCGAAACACTCAGGGAACTCAcagaagagaaagaaaaggaggcaCAGAACCGTGTTCACATCGCATCAACTGGAGGAGCTCGAAAAGGCATTCCATGAAGCACATTACCCAGACGTATATGCCAGGGAAATGTTAGCAATGAAGACAGAATTGCCCGAGGACAGAATACAGGTATGGTTCCAGAATCGTCGGGCCAAGTGGAGAAAACGTGAGAAGTGCTGGGGACGCAGCAGTGTGATGGCAGAGTATGGGCTCTACGGTGCCATGGTCCGCCACTCCATCCCTCTGCCAGAATCAATCATCAACTCCGCCAAGAGCGGGATGATGGGCTCCTGTGCTCCCTGGCTTCTAGGTGAGCCAGCAGGAATGCACAAGAAGTCCATGGAGATTGTAAAGCAATCCCCAGGTACGCCAGAGTCTTCCCACTCGGAAACTTACTCGGAGGAAACTAAAGGGAAAGACAGCGACATGTCCTGGCCCAGCCGCGCTAGTGCTGTAGACGACAGTGAGGACATGGCAATAGACCTATCCAGCACCTCCAAGCAGGACAGCAACAAGAGCACTTTCAAATCATTGTCGCCGCAGAGGGATCTCGTTCCCAACAGTGATTCAGACGATGAGAGCTAAATAGACGTCAATCCCCGTTGCAGACAGTGAGCTCGGACATTTGCGTGGAAATGATGCTCACCTCGAAGAcaattcccactgggcacagacgtcaagtcaacgtctattccacattggttcaacgtaatttcactGAATGACGAGGAAACAACgatgattcaaccagtgtgcgcCTTGTGGGTTATTTTCCAAAGATGTGCAACGGTCCCATCAATTTAGGAGTGTACAGTGTACTTGTCTTATTTCTTAATACTTGTATTTGAACATATGTTTTATAACCTTGTCTGGTTTTAAATAAGATACTATTTAATGTTTTATTCCTTTCTATGCttttgttacatttttttgtgGTATTGAAATAATATTTcaagaaagaagagaaaggacCACCagaaatacacatacacaaacacatttcTCTGAAAACAATTACTGAAAATTACAAACCTTACatcttatttcatatttttgaatGTTGATGGTTAGGGTGTAAGCCCCATCGCCTGCATTTTGTATAAAACATCAACTAAAATACACAGATCATCGTTATCAATGGGCGAAATTAAGCACTTTAGTTGTGTTGATACTGAATGTCATGCTGCATTCAGAGGTCAATTCCACTGTAATGACAGCGAAAATAAGAACAGCAATATCATGAAAacagtcaaataaataaaatctttt
>XM_021608857.2
CCCGCCTCATCACCCCGAGCTacaggagaaagagaaagtagCGCTTTACAATGACAACCATGACAGGAAGAGATGATGGCTCGGATGAAAAGCCCAAAGTCAAGATGCTGGCTCCATCATTTGGGATCGATAAGTCACGACTTCATGGATCTGGGTTTAGGTCTAAAGGCTTTGCCATCACGGACCTACTGGGTCTTGAAACGGATCTCCAGCCTCGCCCATCCGGACCTCATGGAGTAGGAGGTAACGGGGATATTCAGAGCACTGGGATGGGATTCCCTTTCGCTGGAGGATCCTTGCCGcttggtctagggtttctgtgcAGTTTGGCGGCTCAGCAACCTGCGGGAGCCCCCTGCTTCCTACCGAGTCACATACCCCTCCTTCAGTCCAGGACCGAGAGTCATTTCATGCAGAACTTGGAGCAACAAAGAGACCCCTACTCTGATGATGAATGTCTCTCTGGTGATCGAAACGATTCGAAACACTCAGGGAACTCAcagaagagaaagaaaaggaggcaCAGAACCGTGTTCACATCGCATCAACTGGAGGAGCTCGAAAAGGCATTCCATGAAGCACATTACCCAGACGTATATGCCAGGGAAATGTTAGCAATGAAGACAGAATTGCCCGAGGACAGAATACAGGTATGGTTCCAGAATCGTCGGGCCAAGTGGAGAAAACGTGAGAAGTGCTGGGGACGCAGCAGTGTGATGGCAGAGTATGGGCTCTACGGTGCCATGGTCCGCCACTCCATCCCTCTGCCAGAATCAATCATCAACTCCGCCAAGAGCGGGATGATGGGCTCCTGTGCTCCCTGGCTTCTAGGAATGCACAAGAAGTCCATGGAGATTGTAAAGCAATCCCCAGGTACGCCAGAGTCTTCCCACTCGGAAACTTACTCGGAGGAAACTAAAGGGAAAGACAGCGACATGTCCTGGCCCAGCCGCGCTAGTGCTGTAGACGACAGTGAGGACATGGCAATAGACCTATCCAGCACCTCCAAGCAGGACAGCAACAAGAGCACTTTCAAATCATTGTCGCCGCAGAGGGATCTCGTTCCCAACAGTGATTCAGACGATGAGAGCTAA

Function

symbol description
vsx1 Enables chromatin binding activity and transcription cis-regulatory region binding activity. Acts upstream of or within several processes, including negative regulation of axial mesodermal cell fate specification; nervous system development; and paraxial mesodermal cell fate specification. Predicted to be active in nucleus. Is expressed in blastomere; immature eye; nervous system; and neural tube. Human ortholog(s) of this gene implicated in corneal dystrophy; keratoconus; and posterior polymorphous corneal dystrophy 1. Orthologous to human VSX1 (visual system homeobox 1).

NR:

description
visual system homeobox 1 isoform X2

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:0007601 visual perception biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function

KEGG:

id description
K09335 VSX1; visual system homeobox protein 1

RNA

RNA id representative length rna type GC content exon number start site end site
XM_021608848.2 False 1790 mRNA 0.46 5 67288562 67291218
XM_021608857.2 True 1094 mRNA 0.52 5 67289246 67291218

Neighbor

gene id symbol gene type direction distance location
acss1 acss1 coding downstream 17323 67252292 ~ 67271239 (-)
LOC110527505 apmap coding downstream 53128 67226729 ~ 67235434 (-)
LOC110527477 LOC106576725 coding downstream 152773 67068696 ~ 67135789 (-)
si:dkeyp-121d4.3 LOC106576728 coding downstream 229595 67039268 ~ 67096685 (-)
znf318 znf318 coding downstream 249730 67014465 ~ 67038832 (-)
LOC110527584 LOC106576720 coding upstream 95529 67386509 ~ 67389299 (-)
abhd12 LOC106576716 coding upstream 124521 67415739 ~ 67443770 (-)
ninl ninl coding upstream 155223 67446441 ~ 67499228 (-)
LOC118966711 LOC106606039 coding upstream 223542 67514760 ~ 67515221 (-)
LOC118965291 NA coding upstream 224068 67515286 ~ 67516815 (-)
G74699 NA non-coding downstream 16606 67271734 ~ 67271956 (-)
G74693 NA non-coding downstream 50995 67237109 ~ 67237567 (-)
G74692 NA non-coding downstream 52235 67236116 ~ 67236327 (-)
G74688 NA non-coding downstream 62871 67225402 ~ 67225691 (-)
G74711 NA non-coding upstream 1918 67293136 ~ 67293369 (-)
G74715 NA non-coding upstream 7012 67298230 ~ 67298971 (-)
G74739 NA non-coding upstream 38517 67329735 ~ 67330005 (-)
G75208 NA non-coding upstream 45934 67337152 ~ 67337527 (-)
G75214 NA non-coding upstream 52760 67343978 ~ 67344526 (-)
LOC110527436 ppp2r5d other downstream 277975 66965664 ~ 67010646 (-)
tjap1 tjap1 other downstream 465746 66806836 ~ 66883731 (-)
LOC110526867 LOC100136521 other downstream 2907206 64369803 ~ 64384521 (-)
G70013 NA other downstream 4010810 63277208 ~ 63277752 (-)
G69210 NA other downstream 4870266 62411522 ~ 62418296 (-)
LOC110527687 sncg other upstream 378371 67669589 ~ 67681775 (-)
sdhaf4 LOC106576700 other upstream 866743 68157900 ~ 68162024 (-)
G75682 NA other upstream 918962 68210180 ~ 68211706 (-)
LOC110527951 coda1 other upstream 1284375 68575379 ~ 68690343 (-)

Expression


Co-expression Network