XLOC_000580 (sox1b)


Basic Information

Item Value
gene id XLOC_000580
gene name sox1b
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007112.7
NCBI id CM002885.2
chromosome length 59578282
location 46194333 ~ 46196107 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00001011
AAGTAGCTCAAAGACAATTCCACACTGGATGTGAAAATCACGCCGAGAGGAAGTTCGAATAAAACAAAGGGAGTCGAGCTGCCGCAAACTTACCATCCATCATCTGTTTGGATTGTACCGATCTCCTGTTCCAGTGGCCTCTTTTGTTATTAGGAGGTTCTGCGCGCGTGTGTGCCTGCCAGGGGAACGGTGTGAATGTTTCTGTGTGTGAGCTGAGCAAGTCAAAGCCAGGTGAATGTATAGCATGATGATGGAGACGGACTTGCACTCTCCAGGAGCCCAGACTAACACAAACACGGGTCACACGGGACCCAACAGCGGCAGCAAAGTTAACCAAGACCGCGTTAAGAGACCCATGAACGCCTTTATGGTGTGGTCTCGGGGTCAGCGCAGAAAAATGGCTCAGGAGAACCCAAAGATGCACAACTCCGAGATCAGCAAGCGCCTCGGGGCGGAGTGGAAACTCATGTCCGAGGCGGAAAAGCGACCCTTCATCGACGAGGCGAAACGGCTGCGCGCCATGCACATGAAGGAGCATCCGGATTACAAGTACCGGCCCCGGAGGAAGACCAAGACGCTGCTCAAAAAGGACAAGTACTCTTTGGCGGGTGGCCTGCTCGCTGGATCAGGGGGCGGAGGTGGCGTGGGGCTGGGAATGGGTGCAGCGGGGGTCGGCCAGAGGTTAGAGAGTCCGGTGGGTCACGGCGGGAGCACCGCGGCGAGCTACGCGCACATGAACGGCTGGACCAACGGCGCGTACTCGGGCCAGGTGGCAGCCGCAGCGGCAGCAGCCGCAATGATGCAGGAGGCTCAGCTCGCGTACGGTCAGCACCCGGGCAGCGGAGCGCATCACCACCACGGGCACCACCACCATCCACACAACCCCCAGCCTATGCACCGCTACGAAATGACAGCTCTCCAGTACAGCCCCCTCTCAAACTCTCAGAGTTACATGAGCGCCTCGCCTTCAGGATATGGGGGGATATCCTACACACAACACCAAAACTCGAGTGTGGCGTCGTCTGGGGCCATCGGCGCGCTGGGCTCGCTGGTCAAATCGGAGCCAAGCGTAAGCCCTCCCGTTAACGCGCACTCTCGAGCCCCCTGTTCCGGAGACTTGCGAGAGATGATAAGCATGTATTTACCGACGGCGGAGGCGGGGGATCCGTCCGTCCAGAGCAGACTTCACGCTGTACCCCAACACTATCAAAGTTCCACGACGAGCGTAAACGGAACCGTTCCACTGACACACATATGAAACAACTACGCATTCAGACTCAAATAACCAAATATTTACCTCTTTTAGAGCATAACTACCTTTTTGTACAGAATGTCTGTTCTTGTAAATTTGAAGgtgatattatttaattataatacttAAGGGTGTCCTTGGGATGTTGTCTGATAATTTGTCCGAAATGATACAGTATGAGTGAGCTTTTTTTGCGAGGGATTAATTCTTCTTTTGTGAGTGTGAGAGATTCTGTTAAAACGCGAATAAGAGTGGGTGCTTCAGTGTATAGTCAAatacaatgtttttaaagttttctaAGATTTTTCTCGATCCCACTTTGATTTGTCAACACGTGAGTTGCTGTATTTGATCtattacttatttgtttgttgtatttttttccttGTACATTgtgaatataggctattacaGAGAAGAGATTGATAAAACATCTGTAAATATATTTCGGATTTGCCAGGGGATAAAAAGGAAACGTTTTGCGTTGATGTGAGAAGAATAAATTTCACTGGTTTTGCTCTGA

Function

symbol description
sox1b Contributes to DNA-binding transcription factor activity. Acts upstream of or within positive regulation of DNA-binding transcription factor activity. Predicted to be located in nucleus. Predicted to be part of transcription regulator complex. Is expressed in central nervous system; forebrain neural keel; and solid lens vesicle. Orthologous to human SOX1 (SRY-box transcription factor 1).

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0030154 cell differentiation biological_process
GO:0007275 multicellular organism development biological_process
GO:0009653 anatomical structure morphogenesis biological_process
GO:0007399 nervous system development biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II 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:0003677 DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-060322-5 Contributes to DNA-binding transcription factor activity. Acts upstream of or within positive regulation of DNA-binding transcription factor activity. Predicted to be located in nucleus. Predicted to be part of transcription regulator complex. Is expressed in central nervous system; forebrain neural keel; and solid lens vesicle. Orthologous to human SOX1 (SRY-box transcription factor 1).

Ensembl:

ensembl_id ENSDARG00000008131

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00001011 True 1775 mRNA 0.51 1 46194333 46196107

Neighbor

gene id symbol gene type direction distance location
XLOC_000579 NA coding upstream 41133 46032720 ~ 46153200 (+)
XLOC_000578 si:ch211-138g9.2 coding upstream 163756 46026457 ~ 46030577 (+)
XLOC_000577 eif5b coding upstream 173608 45925150 ~ 46020725 (+)
XLOC_000576 lipt1 coding upstream 270329 45922699 ~ 45924004 (+)
XLOC_000575 NA coding upstream 324836 45867040 ~ 45869497 (+)
XLOC_000581 NA coding downstream 21396 46217503 ~ 46219161 (+)
XLOC_000582 NA coding downstream 51511 46247618 ~ 46248591 (+)
XLOC_000583 NA coding downstream 53872 46249979 ~ 46251824 (+)
XLOC_000584 NA coding downstream 67344 46263451 ~ 46272326 (+)
XLOC_000585 NA coding downstream 110908 46307015 ~ 46307550 (+)
XLOC_000573 BX511120.1 non-coding upstream 425803 45768416 ~ 45768530 (+)
XLOC_000568 NA non-coding upstream 546087 45644766 ~ 45648246 (+)
XLOC_000567 NA non-coding upstream 795512 45383604 ~ 45398821 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000119_02031570_02032574 SOX1A, SOX1B, SOX1 coding CI01000119 null 2030668 ~ 2032731 (-)
bowfin (Amia calva) AMCG00014370 sox1a,LOC105893305,LOC106586732,LOC101064967,LOC107692134,LOC107718482 coding CM030128.1 CM030128.1 11392389 ~ 11393405 (+)