sox2 (sox2)


Basic Information

Item Value
gene id sox2
gene name sox2
gene type coding
species rainbow trout (Oncorhynchus mykiss)
category of species economic fish

Chromosome Information

Item Value
chromosome id NC_048569.1
NCBI id CM023223.2
chromosome length 100798064
location 67622271 ~ 67624355 (+)
genome version USDA_OmykA_1.1_2020_rainbow_trout_Genome

Sequence

>XM_021604009.2
ACACAATCCTGGCCGAGGGAACAGTCGCTCTGTGATTGGTCAGGTAAAAAGGCATTTATTCCCTGACAGCCCTCATCACATGAATGGTTGTCTATTAACTTGTTCAAAAAGTATCAGGAGTTGTCAAGGCTCTGGCGGAGAGGGAAAGGTAGTTTGTTGATTCTTTGAGACCAAGAGAGAAGTTTGTGGACACAACAGGACCTACTGGCTCAAAGCAAAAAGACGTTTACTATTTCTACAAAGTTACTGAAAACGACAAGGTAACTCCAGCTAACTGCCTTTTGAGTTGGACTTTTTCAATTGGTCGGGCAAATTTAATACAAATCTGTTAATAATGTATAACATGATGGAAACTGAACTGAAACCCCCCGCACCCCAGACAAATTCTGGGGGTACTGGGAATTCAAATTCATCTGGAAACAACCAGAAAAACAGCCCGGACCGAGTCAAGAGACCCATGAATGCCTTCATGGTTTGGTCAAGGGGACAACGAAGAAAGATGGCACAGGAAAACCCCAAAATGCACAATTCGGAAATAAGCAAAAGACTTGGGGCAGAGTGGAAGCTTCTATCTGAGAGCGAAAAGCGACCTTTCATTGACGAAGCGAAGCGTCTCCGGGCTCTCCACATGAAGGAACATCCGGATTACAAATACCGACCCCGGAGGAAAACCAAGACGCTGATGAAGAAGGACAAGTACACTCTGCCAGGTGGGCTTCTTGCACCGGGCGGCAATGGCATGGGCGCGGGAGTGGGTGTAGGGGGAGGCTTGGGTGGTGGTGTTAATCAAAGGATGGACAGTTACGCACATATGAACGGCTGGACAAATGGAGGTTATGGCATGATGCAGGAGCAGCTTGGCTACGGGCAGCACCCTGGTTTAAACGCTCACAACAACGCGCAGATGCAGCAAATGCACCGCTATGACATGAGCGCACTTCAGTACAACTCCATGACTAACTCCCAGACCTACATGAACGGATCACCCACGTATAGCATGTCCTACTCACAGCAGAGCACTCCTGGAATGACTCTGGGCTCCATGGGTTCGGTGGTCAAGTCAGAGTCCAGTTCCAGTCCCCCCGTAGTCACATCGTCGTCTCACTCCAGGGGTGCTCCATGTCAGACAGGAGACCTACGGGACATGATCAGTATGTACTTACCGGGCGCTGAGGTGCCGGAGCAAACTGCTCAAAGCAGACTCCACATGTCCCAACATTACCAGAGCGCACCTGTACCCGGCACGACGATTAATGGCACACTCCCATTATCACATATGTAAATGAACTTTTATAAGAGAAACTGGACTACTCTGGACTATTTTTGTACAGAAAATTTGGGGTGTGAAATGTTGTATAGAACTCAAGGAAAGAACATAAAACGTTTTTGTCTTTCTATTCTAAAGATAAGTTCTAGAGGAACGGTAGGAACTCTGCAAAAGTTTTTCAATGATGTATAAGTTTGGAAAGTAGAAAGTGGGAGAGTCTCAATCAGATGTTTTATTATTGCAATCACCTTTTGTACAGTATTTATCAAAGAAACATAACAATCAGATGTAATGTTTGTAAACTACAAGAGGTTACATTTTTATAATCAGAAAGTCTGCAGCAAAGAAAATGGCAGAATTGAAATTGAGTTCAAGATGCTTATAAAACTGCAAACATTGGAATAGCGGTAGAAAAAGCAAAGCAGGTAAATGTTTCTCCTTGAGGGTCATTAGTACTAAACCATTTtaatttcctttaaaaaaaagaagaagaagcggAAACCTTTCCTTGCAGGTTAAGCATAATTGTTAATTTATATTTTGTCTCCCACTTTTCATCTGTTAGAGGTATAAAGTTTGTGTTCTTTATTTTCTAATGATTTGTACGATTTATGTATATTTACTGTGATATTTTAAGTTTTTATTTCAAATTTCATTCCCGTAGTTGTATTTTAAATGTTGGCCTGTACGCAGCTGCCAACActtcatgtatatatatattcgaACTAATATCATAATTATAACAGTTACAATTTCAGCTGAGTTTTTTCAATATGCAGTTTGAAATGAATAAATTTTTGAAATTTGGATACTTGAAA

Function

symbol description
sox2 Enables chromatin binding activity and sequence-specific DNA binding activity. Contributes to DNA-binding transcription factor activity. Acts upstream of or within several processes, including animal organ development; fin regeneration; and otic placode development. Predicted to be located in cytoplasm and nucleus. Predicted to be part of transcription regulator complex. Is expressed in several structures, including immature eye; nervous system; neural keel; neural rod; and presumptive structure. Human ortholog(s) of this gene implicated in breast cancer; nasal cavity cancer; and syndromic microphthalmia 3. Orthologous to human SOX2 (SRY-box transcription factor 2).

NR:

description
Transcription factor Sox-2

GO:

id name namespace
GO:0048592 eye morphogenesis biological_process
GO:0031101 fin regeneration biological_process
GO:0051091 positive regulation of DNA-binding transcription factor activity biological_process
GO:0005634 nucleus cellular_component
GO:0005667 transcription regulator complex cellular_component
GO:0005737 cytoplasm cellular_component
GO:0003677 DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function

KEGG:

id description
K16796 SOX2; transcription factor SOX2 (SOX group B)

RNA

RNA id representative length rna type GC content exon number start site end site
XM_021604009.2 True 2085 mRNA 0.42 1 67622271 67624355

Neighbor

gene id symbol gene type direction distance location
fxr1 fxr1 coding upstream 110866 67491153 ~ 67511405 (+)
LOC110524407 LOC106613876 coding upstream 159141 67458540 ~ 67464323 (+)
LOC110524406 LOC106613873 coding upstream 172575 67426327 ~ 67449696 (+)
LOC110524404 LOC106613872 coding upstream 333286 67080011 ~ 67288985 (+)
trnaa-ugc-14 NA coding upstream 582154 67040047 ~ 67040117 (+)
lrrc40 lrrc40 coding downstream 178474 67802829 ~ 67810322 (+)
depdc1a LOC106613883 coding downstream 362824 67987179 ~ 67995354 (+)
LOC110524415 LOC106613887 coding downstream 371999 67996354 ~ 68000277 (+)
LOC110524419 LOC106613886 coding downstream 385836 68010191 ~ 68052897 (+)
LOC110524422 gsh0 coding downstream 569397 68193752 ~ 68200853 (+)
G430297 NA non-coding upstream 180261 67441733 ~ 67442010 (+)
G430285 NA non-coding upstream 186098 67435867 ~ 67436173 (+)
G430282 NA non-coding upstream 193384 67428684 ~ 67428887 (+)
G430279 NA non-coding upstream 194098 67427790 ~ 67428173 (+)
G430744 NA non-coding downstream 349205 67973560 ~ 68002686 (+)
G430749 LOC106613888 non-coding downstream 434198 68058553 ~ 68058967 (+)
G430775 NA non-coding downstream 443909 68068264 ~ 68068617 (+)
G430787 NA non-coding downstream 464789 68089144 ~ 68089356 (+)
G429156 NA other upstream 574107 66981949 ~ 67048164 (+)
G428696 NA other upstream 1479666 66142079 ~ 66142605 (+)
G427747 NA other upstream 2100891 65453856 ~ 65521380 (+)
LOC110524338 LOC106584398 other upstream 2593569 65024444 ~ 65028828 (+)
G430796 LOC106613888 other downstream 478824 68103179 ~ 68103534 (+)
LOC110524423 LOC106613476 other downstream 588361 68212224 ~ 68214236 (+)
G434653 NA other downstream 3335255 70959610 ~ 70959932 (+)
G434792 LOC106613943 other downstream 3594434 71218789 ~ 71223578 (+)
G434829 NA other downstream 3674260 71298615 ~ 71298900 (+)

Expression


Co-expression Network