sox1a SRY-box transcription factor 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sox1aprovided by ZNC
Official Full Name: SRY-box transcription factor 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040718-186
See related: Ensembl:ENSDARG00000069866 AllianceGenome:ZFIN:ZDB-GENE-040718-186
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: fi38c08; fj38h03; zgc:92865; wu:fi38c08; wu:fj38h03
Summary: Contributes to DNA-binding transcription factor activity. Acts upstream of or within determination of left/right symmetry and 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). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 9

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	9	NC_007120.7 (21722734..21724661)
105	previous assembly	GRCz10 (GCF_000002035.5)	9	NC_007120.6 (21911865..21913792)

Chromosome 9 - NC_007120.7 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?

In this study, the authors show that both the left and right habenula are competent to adopt left-type molecular character and efferent connectivity upon the presence of only a few parapineal cells. This ability to impart left-sided character is lost in parapineal cells lacking Sox1a function, despite the normal specification of the parapineal itself.
Title: Sox1a mediates the ability of the parapineal to impart habenular left-right asymmetry.
sox1a and sox1b have a role in formation of glycinergic interneuron in the spinal cord of zebrafish embryos
Title: The HMG box transcription factors Sox1a and Sox1b specify a new class of glycinergic interneuron in the spinal cord of zebrafish embryos.

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General gene information

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Markers

fi38c08.x1 (e-PCR)
- UniSTS:197421

Sox1 (e-PCR), detects polymorphism
- UniSTS:496717

fj38h03.x1 (e-PCR)
- UniSTS:188503

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
contributes_to DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
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 determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info

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
part_of transcription regulator complex	IC Inferred by Curator more info	PubMed

General protein information

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Preferred Names: transcription factor Sox-1a

Names: SRY (sex determining region Y)-box 1a; SRY-box containing gene 1a; transcription factor SOX1A

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_001002483.2 → NP_001002483.1 transcription factor Sox-1a

See identical proteins and their annotated locations for NP_001002483.1

Status: PROVISIONAL

Source sequence(s)

BC076326

UniProtKB/TrEMBL

B2GNY1

Related

ENSDARP00000092797.3, ENSDART00000102021.5

Conserved Domains (2) summary

cd01388
Location:36 → 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 ...

pfam12336
Location:106 → 194

SOXp; SOX transcription factor