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sox11b SRY-box transcription factor 11b [ Danio rerio (zebrafish) ]

Gene ID: 30603, updated on 29-Jan-2023

Summary

Official Symbol
sox11bprovided by ZNC
Official Full Name
SRY-box transcription factor 11bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-980526-466
See related
Ensembl:ENSDARG00000095743 AllianceGenome:ZFIN:ZDB-GENE-980526-466
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
fc90d10; wu:fb53e02; wu:fc90d10
Summary
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 several processes, including camera-type eye development; negative regulation of smoothened signaling pathway; and regulation of sprouting angiogenesis. Predicted to be located in nucleus. Is expressed in several structures, including axis; gonad; hindbrain neural keel; nervous system; and somite. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 9. Orthologous to human SOX11 (SRY-box transcription factor 11). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
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Genomic context

See sox11b in Genome Data Viewer
Location:
chromosome: 20
Exon count:
1
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 20 NC_007131.7 (30032636..30035292, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 20 NC_007131.6 (30129757..30132413, complement)
103 previous assembly Zv9 (GCF_000002035.4) 20 NC_007131.5 (30058544..30061200, complement)

Chromosome 20 - NC_007131.7Genomic Context describing neighboring genes Neighboring gene inhibitor of DNA binding 2b Neighboring gene ring finger protein 144ab Neighboring gene uncharacterized LOC101884038 Neighboring gene allantoicase

Genomic regions, transcripts, and products

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

General gene information

Markers

Homology

Gene Ontology Provided by ZFIN

Process Evidence Code Pubs
involved_in anatomical structure morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within brain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within camera-type eye morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within closure of optic fissure IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within dorsal/ventral pattern formation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within lens development in camera-type eye IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within negative regulation of smoothened signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within regulation of sprouting angiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within response to wounding IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within retinal rod cell development IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
transcription factor SOX-11b
Names
SRY (sex determining region Y)-box 11b
SRY-box containing gene 11b
etID55462.20

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_131337.1NP_571412.1  transcription factor SOX-11b

    See identical proteins and their annotated locations for NP_571412.1

    Status: PROVISIONAL

    Source sequence(s)
    AJ237813
    UniProtKB/TrEMBL
    Q9I9C7
    Related
    ENSDARP00000122216.1, ENSDART00000141068.2
    Conserved Domains (1) summary
    cd01388
    Location:45112
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007131.7 Reference GRCz11 Primary Assembly

    Range
    30032636..30035292 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)