six4a SIX homeobox 4a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: six4aprovided by ZNC
Official Full Name: SIX homeobox 4aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-010201-2
See related: Ensembl:ENSDARG00000004695 AllianceGenome:ZFIN:ZDB-GENE-010201-2
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: six4b; six4.2; fk50f02; wu:fk50f02
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in anterior migratory muscle precursor stream; inner ear; middle migratory muscle precursor stream; posterior migratory muscle precursor stream; and trunk musculature. Orthologous to human SIX4 (SIX homeobox 4). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: all
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Genomic context

Location:: chromosome: 13

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	13	NC_007124.7 (31636728..31647006, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	13	NC_007124.6 (31506278..31516556, 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?

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General gene information

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Markers

fc71b04.y1 (e-PCR)
- UniSTS:194338

fk50f02.x1 (e-PCR)
- UniSTS:201093

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 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 regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor 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	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: homeobox protein SIX4a

Names: sine oculis homeobox homolog 4.2; sine oculis homeobox homolog 4a; sine oculis homeobox homolog 4b

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_131718.2 → NP_571793.2 homeobox protein SIX4a

See identical proteins and their annotated locations for NP_571793.2

Status: VALIDATED

Source sequence(s)

BC134897, BX537123

UniProtKB/TrEMBL

A0A8M1P6K7, A4IG26

Related

ENSDARP00000126511.1, ENSDART00000135381.3

Conserved Domains (2) summary

cd00086
Location:202 → 256

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:82 → 191

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