six1b SIX homeobox 1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: six1bprovided by ZNC
Official Full Name: SIX homeobox 1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-2308
See related: Ensembl:ENSDARG00000026473 AllianceGenome:ZFIN:ZDB-GENE-040426-2308
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: six1; zgc:77345
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 several processes, including chordate pharyngeal muscle development; nervous system development; and skeletal muscle tissue 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 brain; cephalic musculature; ectoderm; peripheral nervous system; and pharyngeal arch. 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, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 20

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	20	NC_007131.7 (20499923..20501818)
105	previous assembly	GRCz10 (GCF_000002035.5)	20	NC_007131.6 (20600250..20602145)

Chromosome 20 - NC_007131.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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 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?

SIX1 reprograms myogenic transcription factors to maintain the rhabdomyosarcoma undifferentiated state.
Title: SIX1 reprograms myogenic transcription factors to maintain the rhabdomyosarcoma undifferentiated state.
Data demonstrate a new role for miR30a at a key node in the myogenic regulatory gene network through controlling Six1 expression.
Title: MicroRNA-30a regulates zebrafish myogenesis through targeting the transcription factor Six1.
Data show a mechanism for Six1a and Six1b in establishing the Pax7(+) cell derived part of the fast muscle and suggest new important roles for Six1 in the regulation of the Pax7(+) muscle cell population through pSmad1/5/8 signalling.
Title: Six1 regulates proliferation of Pax7-positive muscle progenitors in zebrafish.
six1 promotes inner hair cell fate and inhibits neuronal fate during development.
Title: The transcription factor six1 inhibits neuronal and promotes hair cell fate in the developing zebrafish (Danio rerio) inner ear.

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 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 adenohypophysis development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chordate pharyngeal muscle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within extraocular skeletal muscle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peripheral nervous system neuron development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
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 striated muscle cell differentiation	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 six1b

Names: homeobox protein six1a; homeodomain transcription factor six1; sine oculis homeobox homolog 1; sine oculis homeobox homolog 1a; sine oculis homeobox homolog 1b; six1a

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_207095.1 → NP_996978.1 homeobox protein six1b

See identical proteins and their annotated locations for NP_996978.1

Status: PROVISIONAL

Source sequence(s)

BC066396

UniProtKB/Swiss-Prot

Q05FF5, Q6NZ04

Related

ENSDARP00000028379.4, ENSDART00000036124.7

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