XLOC_012247 (sox11a)


Basic Information

Item Value
gene id XLOC_012247
gene name sox11a
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 35878544 ~ 35881841 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00024131
GGCTTGTAACTCTGGAAAGAGTGGGTGAACCTCTGAGTCGCAGAGAGCAGACGTACACACGGGTTGATATTTTGGACTGACAACGCACGGCAACGGCACCATGGTGCAGCAAACGGACAACAGCGAAACGGACAGCATGTCTAGAGAAGCCACTGACTCTGATGAAAGCGAATTCATGGTCTCGATAAACCCAGACTGGTGCAAGACAGCCACCGGACACATAAAGCGACCGATGAACGCGTTCATGGTGTGGTCTAAAATCGAGCGGAGAAAGATCATGGAACAGTCTCCAGACATGCACAACGCCGAGATCTCCAAACGCTTGGGGAAGCGCTGGAAAATGCTGAAAGACAGCGAAAAGATACCTTTCATCAGGGAAGCCGAGAGACTCCGGTTGAAACACATGGCTGACTACCCCGACTACAAATACAGACCGAAGAAGAAACCAAAGCTGGACAGTTCATCCAAACCTTCAGCCCCGTCTCCGGAAAAGTGCAGCAAGACTTCCAAGAGCTCCAAGAAATGTCCCAAACTGAAAGCGAACAAGACGGGGAGCAAGTCGTCGTCTCACGGCTACGGAGACGAGTACGCGTTCAAGAGCACGAAAGTTTCAAAGACTGTTCACATTAAAAGTGAATTCACGGACGAAGACGACGATGACGACTCCGAGGAGGACTCTCGGGTCAGGGTgaaagaggaggaagaggatCCGATACGAGCCTACAATGTAGCAAAAGTTCCCGCCAGCCCAACTTTGAGCTCGTCCACCGAGTCTGAAGGCGCCAGCATGTACGAGGAGGTCCGGAACAACAGACTCTATTACAACTTCAAAAACATCACCAAGCAGAGCACAATGTATCCCGCATCCGTCTCACCAGCATCCTCTAGGTCCGTTTCCACGTCTTCCAGCTCGAGCGAAGACGCGGACGACTTGCTTTTTGACTTCAGTTTGAACTTCGCCTCCTCCGCGCAAAGCTCGGAGCTGGGCAGCCAAAATCCAGGgaatctctccctctctctggtGGATAAGGAGTTGGAGTCTTTTAGCGAGGGCAGCCTGGGCTCCCACTTTGAATTTCCAGACTATTGCACGCCTGAGCTCAGCGAAATGATAGCTGGGGACTGGCTCGAAGCGAACTTTTCGGACTTGGTTTTTACATACTAAATAAGACTATTCCCAAGTAATAACACACACGGGAGAGAGGTATAATGCTCTGTTCTGTACGTATTTCTTTCCCCTGCCTTCCACTGCTGGTCCACCTATAGGGGTTTTGGGACGAAGGCGCGTATGGCAAGCTGTTTAAACGTTTATTTCTAGAAACTACTTTGTGTCTATCAGTACATTTTTTAAACTGCAAGTAATTCAGATGTGAATAGtatgtttttttgctttttaaaggaaaaaaaatgtgattacCAAAAAAATGTGACTGTGTTATTACAATGGACAGTTAACCAggaataataactaattaaaatagTACTGGTTGCTCAGTAAACACAGCAGCATTTGGAGACACGTCAAAAGATATAGCAAAggtatatgaaataaataaactatttaaagaaCAATCGGTAGtgaaaataataagataaaatgtatagtttgtattGGATTGCTTTCAtgtaattaagtaataataacgAAACAGATACTTTTTAGTTTGAAGgtataaatgttaaaatggcttgccataagGCAGGGAGAGGTTTGAGGATTTAGATGCTCATGAAGCTGGtactgtagcaaaaaaaaaaagaaaaaaagaaaaaagtctgcggacatttttcccccttttttttctgGCAGCATGACAGGGTTTTATGGATTTTTCTGTAGGTCTACAATTACTGTTCAACTAAAGCGGACCACAAAGGGAAAATCTGAGAACTTCTATGCATCTTATACCCTCTTTCTAACTGCAGGGAGCTGAAAATGTAAAGACTGTGGACTGACTCAAAGCAAATCTGTGAACTATTACTGTTCAGgacatttcttttaaaatgttgttcAGTCATTTCTAAATAccggattttttttctttacttttcttttatttttttagtgatTCTGATTCTGTTTACCTACTGGTTTGAAACTTAAGCAGCCTAAACCTCCTTAGAGTTGCAGGTGTTCGAGGAAGCATTTTGATACATAACAGACCTCATCTTTTTAAAAGAAAGCAAACTATTTTCAGGCATATTTTTGTACAGTTACAAAGGGAATGTTCTTACTGGGCACTCAGTGAGTTTCAGGCACTTCTTCCctttatcatttgttttaaagCATGCAAGGGAGTCCTGGTTTAAGgattaagtttaaattaaaacttGCATCAAAAATGCCTTGTGATTTTAAGCTAGGTTTTGTACAGCTGTAGATCAAATTTGTTGAGTATTTGTAGGACATATGGCATTGGGGAGGGAGGAGATGTATACCTCAGTGCTGGTATTAGTTTCAAGATTGTATATGTACTGTAAAATAGTAAAGTTAGGAGTTTATGTATATCATACTCGTGATATGTGGATGGGTCCCAAATCGCAGGTGTGAGACTGGAtttgttatcttttttttatttttttattttttatggcaCATACTGTTTCCCCTTCATTTTTTGTGCAATATATTTACTTGTAAATGCAGAccatctacattttttttttgcatttttgtagCAAAATGATGGACAGGCAGCGTTCTGCTGTGTTAACATCATTATTTGTCATAATGCTGAAGTCATTGATGAATAAAGAAATCAGCTGGAACTGATCGTAACTGAATATGGTCACACAGTGTGCTTTTCTGTGGAGGAAAAACCCCACCATTTCTCTTCAAACTGACCCACAAATTTGGACAATCTACGTCCTGCAGCCAATTTGAATATGActcgttattttattttatatttttgaatatgTGCCATAATGGGCAAATAATGAATGTCGGTGGTCtggctgaagaaaaaaaaaaaaaaaaacaagaaagcaaAAAAGGTACATTCCATATCCTTGTTTCATATGATGAAACTTTTATTTTCAACTCAAGACTGCCGTCttttctattaaaaacaacaactacaacaaccataaacctgtatttttgtttcttgcacttaaacatattttgtttatttttatgtgggTCTGACATGAAGTCTGTTTTTGATACAAGGTTTGGAATATGATAGACTCTTTGCCAGGGAACATGGTGAAGCAAGGCAGCCTATAGCCTCACATTCCAAATGTGAACCTCTCTTTGACTCatcttttaataaacaaatacttaCCACCATAA
>TCONS_00024545
GGCTTGTAACTCTGGAAAGAGTGGGTGAACCTCTGAGTCGCAGAGAGCAGACGTACACACGGGTTGATATTTTGGACTGACAACGCACGGCAACGGCACCATGGTGCAGCAAACGGACAACAGCGAAACGGACAGCATGTCTAGAGAAGCCACTGACTCTGATGAAAGCGAATTCATGGTCTCGATAAACCCAGACTGGTGCAAGACAGCCACCGGACACATAAAGCGACCGATGAACGCGTTCATGGTGTGGTCTAAAATCGAGCGGAGAAAGATCATGGAACAGTCTCCAGACATGCACAACGCCGAGATCTCCAAACGCTTGGGGAAGCGCTGGAAAATGCTGAAAGACAGCGAAAAGATACCTTTCATCAGGGAAGCCGAGAGACTCCGGTTGAAACACATGGCTGACTACCCCGACTACAAATACAGACCGAAGAAGAAACCAAAGCTGGACAGTTCATCCAAACCTTCAGCCCCGTCTCCGGAAAAGTGCAGCAAGACTTCCAAGAGCTCCAAGAAATGTCCCAAACTGAAAGCGAACAAGACGGGGAGCAAGTCGTCGTCTCACGGCTACGGAGACGAGTACGCGTTCAAGAGCACGAAAGTTTCAAAGACTGTTCACATTAAAAGTGAATTCACGGACGAAGACGACGATGACGACTCCGAGGAGGACTCTCGGGTCAGGGTgaaagaggaggaagaggatCCGATACGAGCCTACAATGTAGCAAAAGTTCCCGCCAGCCCAACTTTGAGCTCGTCCACCGAGTCTGAAGGCGCCAGCATGTACGAGGAGGTCCGGAACAACAGACTCTATTACAACTTCAAAAACATCACCAAGCAGAGCACAATGTATCCCGCATCCGTCTCACCAGCATCCTCTAGGTCCGTTTCCACGTCTTCCAGCTCGAGCGAAGACGCGGACGACTTGCTTTTTGACTTCAGTTTGAACTTCGCCTCCTCCGCGCAAAGCTCGGAGCTGGGCAGCCAAAATCCAGGgaatctctccctctctctggtGGATAAGGAGTTGGAGTCTTTTAGCGAGGGCAGCCTGGGCTCCCACTTTGAATTTCCAGACTATTGCACGCCTGAGCTCAGCGAAATGATAGCTGGGGACTGGCTCGAAGCGAACTTTTCGGACTTGGTTTTTACATACTAAATAAGACTATTCCCAAGTAATAACACACACGGGAGAGAGGTATAATGCTCTGTTCTGTACGTATTTCTTTCCCCTGCCTTCCACTGCTGGTCCACCTATAGGGGTTTTGGGACGAAGGCGCGTATGGCAAGCTGTTTAAACGTTTATTTCTAGAAACTACTTTGTGTCTATCAGTACATTTTTTAAACTGCAAGTAATTCAGATGTGAATAGtatgtttttttgctttttaaaggaaaaaaaatgtgattacCAAAAAAATGTGACTGTGTTATTACAATGGACAGTTAACCAggaataataactaattaaaatagTACTGGTTGCTCAGTAAACACAGCAGCATTTGGAGACACGTCAAAAGATATAGCAAAggtatatgaaataaataaactatttaaagaaCAATCGGTAGtgaaaataataagataaaatgtatagtttgtattGGATTGCTTTCAtgtaattaagtaataataacgAAACAGATACTTTTTAGTTTGAAGgtataaatgttaaaatggcttgccataagGCAGGGAGAGGTTTGAGGATTTAGATGCTCATGAAGCTGGtactgtagc
>TCONS_00024947
ATGGTGCAGCAAACGGACAACAGCGAAACGGACAGCATGTCTAGAGAAGCCACTGACTCTGATGAAAGCGAATTCATGGTCTCGATAAACCCAGACTGGTGCAAGACAGCCACCGGACACATAAAGCGACCGATGAACGCGTTCATGGTGTGGTCTAAAATCGAGCGGAGAAAGATCATGGAACAGTCTCCAGACATGCACAACGCCGAGATCTCCAAACGCTTGGGGAAGCGCTGGAAAATGCTGAAAGACAGCGAAAAGATACCTTTCATCAGGGAAGCCGAGAGACTCCGGTTGAAACACATGGCTGACTACCCCGACTACAAATACAGACCGAAGAAGAAACCAAAGCTGGACAGTTCATCCAAACCTTCAGCCCCGTCTCCGGAAAAGTGCAGCAAGACTTCCAAGAGCTCCAAGAAATGTCCCAAACTGAAAGCGAACAAGACGGGGAGCAAGTCGTCGTCTCACGGCTACGGAGACGAGTACGCGTTCAAGAGCACGAAAGTTTCAAAGACTGTTCACATTAAAAGTGAATTCACGGACGAAGACGACGATGACGACTCCGAGGAGGACTCTCGGGTCAGGGTgaaagaggaggaagaggatCCGATACGAGCCTACAATGTAGCAAAAGTTCCCGCCAGCCCAACTTTGAGCTCGTCCACCGAGTCTGAAGGCGCCAGCATGTACGAGGAGGTCCGGAACAACAGACTCTATTACAACTTCAAAAACATCACCAAGCAGAGCACAATGTATCCCGCATCCGTCTCACCAGCATCCTCTAGGTCCGTTTCCACGTCTTCCAGCTCGAGCGAAGACGCGGACGACTTGCTTTTTGACTTCAGTTTGAACTTCGCCTCCTCCGCGCAAAGCTCGGAGCTGGGCAGCCAAAATCCAGGgaatctctccctctctctggtGGATAAGGAGTTGGAGTCTTTTAGCGAGGGCAGCCTGGGCTCCCACTTTGAATTTCCAGACTATTGCACGCCTGAGCTCAGCGAAATGA

Function

symbol description
sox11a Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within brain development; camera-type eye development; and negative regulation of smoothened signaling pathway. Predicted to be located in nucleus. Is expressed in several structures, including mesoderm; nervous system; neural keel; neural rod; and somite. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 9. Orthologous to human SOX11 (SRY-box transcription factor 11).

GO:

id name namespace
GO:0061386 closure of optic fissure biological_process
GO:0046548 retinal rod cell development biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0030154 cell differentiation biological_process
GO:0030182 neuron differentiation biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0002088 lens development in camera-type eye biological_process
GO:0009653 anatomical structure morphogenesis biological_process
GO:0048593 camera-type eye morphogenesis biological_process
GO:0045879 negative regulation of smoothened signaling pathway biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0007420 brain development biological_process
GO:0005634 nucleus cellular_component
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific molecular_function
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-980526-395 Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within brain development; camera-type eye development; and negative regulation of smoothened signaling pathway. Predicted to be located in nucleus. Is expressed in several structures, including mesoderm; nervous system; neural keel; neural rod; and somite. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 9. Orthologous to human SOX11 (SRY-box transcription factor 11).

Ensembl:

ensembl_id ENSDARG00000077811

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00024131 False 3298 mRNA 0.40 1 35878544 35881841
TCONS_00024545 False 1748 lncRNA 0.46 1 35880094 35881841
TCONS_00024947 True 1012 lncRNA 0.52 1 35880730 35881741

Neighbor

gene id symbol gene type direction distance location
XLOC_012245 BX255944.2 coding downstream 32288 35554571 ~ 35846256 (-)
XLOC_012246 BX255944.1 coding downstream 260440 35617986 ~ 35618104 (-)
XLOC_012244 rsad2 coding downstream 517222 35357451 ~ 35361322 (-)
XLOC_012243 rnf144aa coding downstream 525854 35285876 ~ 35352690 (-)
XLOC_012242 adam17a coding downstream 599122 35247497 ~ 35279422 (-)
XLOC_012248 AL929378.2 coding upstream 19224 35901065 ~ 36340579 (-)
XLOC_012249 NA coding upstream 564673 36446514 ~ 36476734 (-)
XLOC_012250 NA coding upstream 600746 36482587 ~ 36513936 (-)
XLOC_012251 colec11 coding upstream 634854 36516695 ~ 36529449 (-)
XLOC_012252 CR354585.1 coding upstream 753231 36635072 ~ 36635189 (-)
XLOC_012238 NA non-coding downstream 1072786 34706779 ~ 34805758 (-)
XLOC_012237 NA non-coding downstream 1186988 34661398 ~ 34691556 (-)
XLOC_012235 NA non-coding downstream 2306738 33564882 ~ 33571806 (-)
XLOC_012253 BX649242.1 non-coding upstream 791643 36673484 ~ 36675877 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
bowfin (Amia calva) AMCG00003530 LOC108258189,LOC103368564,LOC106533618 coding CM030121.1 CM030121.1 7978775 ~ 7980197 (+)