six6b SIX homeobox 6b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: six6bprovided by ZNC
Official Full Name: SIX homeobox 6bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-050522-308
See related: Ensembl:ENSDARG00000031316 AllianceGenome:ZFIN:ZDB-GENE-050522-308
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: zgc:110344; si:dkey-225h23.3
Summary: Enables double-stranded DNA binding activity. Involved in gene expression. Acts upstream of or within camera-type eye development and cell population proliferation. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in brain; eye; 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: 20

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	20	NC_007131.7 (20531002..20533865, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	20	NC_007131.6 (20631329..20634192, complement)

Chromosome 20 - NC_007131.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

We characterized the effect of the novel loci through pathway analysis and found that pathways involved are not entirely distinct as assumed so far. Further, we identified a novel association between CDKN1A and POAG. Using a zebrafish model we show that six6b (associated with POAG and optic nerve head variation) alters the expression of cdkn1a
Title: New insights into the genetics of primary open-angle glaucoma based on meta-analyses of intraocular pressure and optic disc characteristics.

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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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in eye development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within eye development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gene expression	IGI Inferred from Genetic Interaction 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 SIX6b

Names: sine oculis-related homeobox 6b

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_001020585.1 → NP_001018421.1 homeobox protein SIX6b

See identical proteins and their annotated locations for NP_001018421.1

Status: PROVISIONAL

Source sequence(s)

BX649231

UniProtKB/TrEMBL

E7F8V1, Q503Q3, Q5TYZ2

Related

ENSDARP00000110487.2, ENSDART00000125039.3

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