sox11a SRY-box transcription factor 11a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sox11aprovided by ZNC
Official Full Name: SRY-box transcription factor 11aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-395
See related: Ensembl:ENSDARG00000077811 AllianceGenome:ZFIN:ZDB-GENE-980526-395
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: cb237; id:ibd2104; wu:fb16g02; zgc:136533
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 brain development; camera-type eye development; and negative regulation of smoothened signaling pathway. Predicted to be active in nucleus. Is expressed in several structures, including mesoderm; nervous system; neural keel; pleuroperitoneal region; and somite. Used to study Coffin-Siris syndrome. 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, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 17

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	17	NC_007128.7 (35878547..35881807, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	17	NC_007128.6 (35930942..35934202, complement)

Chromosome 17 - NC_007128.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

This study demonstrated that SOX11a strongly expressed in retinal ganglion cells (RGCs), and knockdown of Sox11a inhibited RGC axon regrowth in retinal explants.
Title: Expression of SoxC Transcription Factors during Zebrafish Retinal and Optic Nerve Regeneration.
Sox11a/b knockdown in zebrafish causes brain abnormalities, potentially explaining the brain phenotype of Coffin-Siris syndrome in humans.
Title: De novo SOX11 mutations cause Coffin-Siris syndrome.
our study reveals a novel role for Sox11 in controlling Hedgehog signaling, and suggests that SOX11 variants contribute to pediatric eye disorders.
Title: Sox11 is required to maintain proper levels of Hedgehog signaling during vertebrate ocular morphogenesis.
the duplicated zebrafish sox11a and -b loci were used to test the duplication, degeneration, complementation model of genome evolution through whole genome duplication.
Title: Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in camera-type eye morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
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 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
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
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retinal rod cell development	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: transcription factor SOX-11a

Names: SRY (sex determining region Y)-box 11a; SRY-box containing gene 11a; etID309973.17

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)

NM_131336.1 → NP_571411.1 transcription factor SOX-11a

See identical proteins and their annotated locations for NP_571411.1

Status: PROVISIONAL

Source sequence(s)

AJ237812

UniProtKB/TrEMBL

A4QP08, F6P1Z4, Q9I9C8

Related

ENSDARP00000105811.2, ENSDART00000110040.4

Conserved Domains (1) summary

cd01388
Location:40 → 107

SOX-TCF_HMG-box; 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 ...