six3b SIX homeobox 3b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: six3bprovided by ZNC
Official Full Name: SIX homeobox 3bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-128
See related: Ensembl:ENSDARG00000054879 AllianceGenome:ZFIN:ZDB-GENE-990415-128
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: SIX3; six6; cb347; six3.2
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 embryonic camera-type eye morphogenesis; nervous system development; and sensory epithelium regeneration. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including hypoblast; immature eye; nervous system; neural keel; and neural rod. Human ortholog(s) of this gene implicated in holoprosencephaly and holoprosencephaly 2. Orthologous to human SIX3 (SIX homeobox 3). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 12

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	12	NC_007123.7 (25600750..25603341)
105	previous assembly	GRCz10 (GCF_000002035.5)	12	NC_007123.6 (25509390..25511981)

Chromosome 12 - NC_007123.7 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?

lmo4b has an essential role in forebrain development as a modulator of six3 and rx3 expression, and thus indirectly influences neural cell fate commitment, cell proliferation and tissue growth in the anterior CNS.
Title: A zebrafish LMO4 ortholog limits the size of the forebrain and eyes through negative regulation of six3b and rx3.
Lhx2 may mediate an alternative or parallel pathway for control of cellular proliferation in the developing forebrain via Six3b.
Title: Lhx2 mediates the activity of Six3 in zebrafish forebrain growth.

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General gene information

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Markers

fa01b08.s1 (e-PCR)
- UniSTS:202114

aa495395 (e-PCR)
- UniSTS:186856

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 brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic camera-type eye morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in eye development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within eye development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within optic nerve development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within optic nerve morphogenesis	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
acts_upstream_of_or_within sensory epithelium regeneration	IGI Inferred from Genetic Interaction more info	PubMed

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 SIX3b

Names: sine oculis homeobox homolog 3b; sine oculis homeobox homolog 6

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_131363.1 → NP_571438.1 homeobox protein SIX3b

See identical proteins and their annotated locations for NP_571438.1

Status: PROVISIONAL

Source sequence(s)

AF030281

UniProtKB/TrEMBL

O73709, Q6PC98

Related

ENSDARP00000071625.4, ENSDART00000077157.5

Conserved Domains (2) summary

cd00086
Location:170 → 218

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:49 → 162

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