six6a SIX homeobox 6a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: six6aprovided by ZNC
Official Full Name: SIX homeobox 6aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-1282
See related: Ensembl:ENSDARG00000025187 AllianceGenome:ZFIN:ZDB-GENE-040426-1282
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: Six6; zgc:63871
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. Acts upstream of or within gene expression and neural retina development. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including eye; gill; heart; integument; and kidney. Human ortholog(s) of this gene implicated in optic disc anomalies with retinal and/or macular dystrophy. Orthologous to human SIX6 (SIX homeobox 6). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 13

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	13	NC_007124.7 (31603988..31606247)
105	previous assembly	GRCz10 (GCF_000002035.5)	13	NC_007124.6 (31473538..31475797)

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?

Six6b and six7 govern expression of the SWS2 and RH2 opsins responsible for middle-wavelength sensitivity.
Title: Six6 and Six7 coordinately regulate expression of middle-wavelength opsins in zebrafish.

Submit: New GeneRIF Correction

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 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 eye development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within gene expression	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within neural retina development	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

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 SIX6a

Names: sine oculis homeobox homolog 6; sine oculis-related homeobox 6a

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_201105.1 → NP_957399.1 homeobox protein SIX6a

See identical proteins and their annotated locations for NP_957399.1

Status: PROVISIONAL

Source sequence(s)

BC053123

UniProtKB/TrEMBL

A0A8M1PFL8, Q7T3G8

Related

ENSDARP00000030834.4, ENSDART00000030646.5

Conserved Domains (2) summary

cd00086
Location:130 → 178

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 → 122

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