six1a SIX homeobox 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: six1aprovided by ZNC
Official Full Name: SIX homeobox 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040718-155
See related: Ensembl:ENSDARG00000039304 AllianceGenome:ZFIN:ZDB-GENE-040718-155
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: six2; six1b; zgc:92332
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific. Acts upstream of or within regulation of inner ear receptor cell differentiation; regulation of skeletal muscle cell proliferation; and skeletal muscle fiber development. Predicted to be located in cytoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including anterior migratory muscle precursor stream; middle migratory muscle precursor stream; musculature system; nervous system; and posterior migratory muscle precursor stream. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 23; branchiootorenal syndrome; and nephroblastoma. Orthologous to human SIX1 (SIX homeobox 1). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 13

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	13	NC_007124.7 (31619961..31622195, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	13	NC_007124.6 (31489511..31491745, complement)

Chromosome 13 - NC_007124.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Balancing cell numbers during organogenesis: Six1a differentially affects neurons and sensory hair cells in the inner ear
Title: Balancing cell numbers during organogenesis: Six1a differentially affects neurons and sensory hair cells in the inner ear.
six1a and pax3 do not function in the same regulatory network. We proposed four putative regulatory pathways to understand how six1a distinctly interacts with either myf5 or myod during zebrafish craniofacial muscle development.
Title: The transcription factor Six1a plays an essential role in the craniofacial myogenesis of zebrafish.
Six1a plays an essential role at the onset of fast muscle differentiation.
Title: Six1a is required for the onset of fast muscle differentiation 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 factor 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 DNA-binding transcription factor activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype 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
acts_upstream_of_or_within apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of inner ear receptor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of skeletal muscle cell proliferation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of skeletal muscle cell proliferation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of skeletal muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal muscle fiber development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within skeletal muscle fiber development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within skeletal muscle fiber development	IMP Inferred from Mutant Phenotype more info	PubMed

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

General protein information

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Preferred Names: homeobox protein six1a

Names: homeobox protein six1b; homeodomain transcription factor Six1b; sine oculis homeobox homolog 1a; sine oculis homeobox homolog 1b; sine oculis homeobox homolog 2

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_001009904.1 → NP_001009904.1 homeobox protein six1a

See identical proteins and their annotated locations for NP_001009904.1

Status: PROVISIONAL

Source sequence(s)

BC076015

UniProtKB/Swiss-Prot

B8A5G7, Q6DHF9

UniProtKB/TrEMBL

A0A8M9QFC5

Related

ENSDARP00000057431.3, ENSDART00000057432.4

Conserved Domains (2) summary

cd00086
Location:129 → 180

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam16878
Location:9 → 118

SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain