XLOC_037088 (sox1a)


Basic Information

Item Value
gene id XLOC_037088
gene name sox1a
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007120.7
NCBI id CM002893.2
chromosome length 56459846
location 21722733 ~ 21724661 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00073008
ATTGGCCGCTCGCTCATTTTAATCGCTGTCAAAACGCATCATATGGCCGCCGCTTTAACTAACTCTTCAACTCCACtaggaaaagtaactcaaatgcACGTTCAATTAATGTGGATGTGAAGCGGCAGTCGGAGACGACACTAAACTGGCTACAGGAGCGAAAAGAGAGCCCGAAATTGTCAGCAAACGGTTGGGAATAAGCTGAATTCCACACTTCATCGGAGCTCCACTGGCTCGTGAAGCACCTGTTTCAAGCGGACTACGGAGCGCCGAAAGTTCATGCTTTTTCTCTGCTAGTTGAGAACTTTTAAGCCACTTGAATGTATAGCATGATGATGGAAACGGACCTTCATTCCCCGGGACCCCAAACCAACACGAACCCGGGGCAAACGGGTCCAAATTCGGGGAGCAAAGCCAATCAAGACCGCGTAAAGAGACCCATGAACGCGTTTATGGTCTGGTCTCGGGGCCAGCGCCGAAAAATGGCACAGGAGAACCCCAAAATGCACAACTCTGAAATTAGCAAAAGACTCGGTGCTGAGTGGAAGGTGATGTCAGAGGCTGAAAAGCGGCCCTTTATTGATGAGGCGAAGCGGTTGCGAGCCATGCACATGAAAGAGCATCCGGATTACAAATACAGACCGAGGCGCAAAACCAAGACCCTGCTTAAAAAGGACAAGTACTCGTTGGCGGGTGGCTTGCTCGGCGGTGCGGGTGGTGGAGTCGGGATGAGTCCTGCGGGGGTCGGCCAGAGGTTGGAGAGTCCTGGGGGTCACGGAGGCTCGGCCAGCGCTGGCTACGCGCACATGAACGGCTGGGCGAACGGCACTTACTCCGGCCAGGTGGCTGCCGCGGCGGCGGCCGCCGCGATGATGCAGGAGGCGCAGCTCGCTTACAGCCAGCACCCCGGCAGTGGCTCTCACCATCACCACGCTCATCACCATCACCCGCACAATCCTCAGCCCATGCACCGCTACGACATGACTGCACTCCAGTACAGCCCCATCTCGAACTCCCAGAGCTACATGAGCGCGTCCCCGTCCGGCTACGGTGGGATATCATACACGCAGCATCAGAACTCCAGCGTCGCGACTTCTGCCGCCATCGGCACGCTGAGCTCGCTCGTCAAGTCCGAACCCAATATCAGTCCCCCGGTTACCACGCACTCCCGAGGCCCTTGCCCCGGAGACTTGAGAGAGATGATTAGCATGTATTTACCGACCGGGGAGTCCGGGGATCCGTCTGTGCAGAGCAGACTGCATGCCTTACCGCAGCACTATCAGAGCACGACTGCCGGAGTAAACGGAACTGTCCCACTGACGCATATTTGAAACAGCTGATGGAAAGCGATGGGTAACGCGCATTCAGAAACACTCCACCAAAAATATTTACCTCTTTTTTTTAGATTGTCATTGAACTACTTTTGTACAGAATGTTTTATGATGTTCTTGTAAATTAAAGGTAAATATTGTTTCGATTGCAGTTCGGAGAGAAACTGAGGTCTTATATCAGATGTATCACTTTCAGTGAAGCATTGTTTAAATATGACGTCTTTAAAATGATCCTGACAGCGTTTCTGGCCTCGCCAAGAAATATGCGACACACTgttattctttaaatatttaagtttctGTGCAGATTGACTTTTAAGTTGATAATGACAAAAGTCTAGCGTGAAGAACTCAATGAAATGTTTTTGAGAGCCCATAAAGAGTTTCCTGCTTATTACATTTACCAAAACGTTTGTATACGTGAATTAATGTACCAGATTTATGTTGTAATATTTCTTGTAAATTGTGAATaagttttaatatttcaaaagGCTGGCACGTCACTGCTGCTGTACATAATTTATGACATGCATTACTGCCAGTTCAAATCTTAACCTTGCGTTGATTCATGGTCTAAATAAAATTGGAGAAAAAGTTA

Function

symbol description
sox1a 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 several structures, including forebrain neural keel; lens placode; nervous system; neural plate; 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-040718-186 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 several structures, including forebrain neural keel; lens placode; nervous system; neural plate; and solid lens vesicle. Orthologous to human SOX1 (SRY-box transcription factor 1).

Ensembl:

ensembl_id ENSDARG00000069866

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00073008 True 1929 mRNA 0.49 1 21722733 21724661

Neighbor

gene id symbol gene type direction distance location
XLOC_037086 BX649266.2 coding upstream 226034 21495873 ~ 21496699 (+)
XLOC_037085 gja3 coding upstream 313267 21407987 ~ 21409466 (+)
XLOC_037084 cryl1 coding upstream 317667 21383620 ~ 21405066 (+)
XLOC_037083 eef1akmt1 coding upstream 359232 21358941 ~ 21363501 (+)
XLOC_037082 xpo4 coding upstream 364892 21306902 ~ 21357841 (+)
XLOC_037089 NA coding downstream 37035 21761696 ~ 21765735 (+)
XLOC_037090 rev1 coding downstream 68904 21793565 ~ 21816606 (+)
XLOC_037091 txndc9 coding downstream 94421 21819082 ~ 21824647 (+)
XLOC_037092 zgc:162944 coding downstream 102063 21826724 ~ 21831588 (+)
XLOC_037093 kctd12.1 coding downstream 119254 21843915 ~ 21845783 (+)
XLOC_037078 pla1a non-coding upstream 496601 21214940 ~ 21226132 (+)
XLOC_037077 NA non-coding upstream 517261 21202272 ~ 21205472 (+)
XLOC_037067 CR456628.1 non-coding upstream 1286218 20433812 ~ 20436515 (+)
XLOC_037066 CR456628.2 non-coding upstream 1330699 20386745 ~ 20392034 (+)
XLOC_037095 CR536604.1 non-coding downstream 259448 21984109 ~ 21985996 (+)
XLOC_037104 NA non-coding downstream 588072 22312733 ~ 22313617 (+)
XLOC_037108 BX548053.3 non-coding downstream 852284 22576945 ~ 22577059 (+)
XLOC_037110 NA non-coding downstream 917725 22642386 ~ 22642685 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000009_09565012_09566010 SOX1A, SOX1B, SOX1 coding CI01000009 null 9564446 ~ 9568007 (-)
bowfin (Amia calva) AMCG00009021 sox2,LOC106584342,LOC107655276 coding CM030126.1 CM030126.1 19260287 ~ 19261111 (-)