six3a SIX homeobox 3a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: six3aprovided by ZNC
Official Full Name: SIX homeobox 3aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-127
See related: Ensembl:ENSDARG00000058008 AllianceGenome:ZFIN:ZDB-GENE-990415-127
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; six3.1; wu:fc10a08
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 brain development and optic nerve morphogenesis. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including anterior neural keel; central nervous system; eye; neural plate; and optic vesicle. 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, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 13

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	13	NC_007124.7 (10258007..10261383, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	13	NC_007124.6 (10125532..10128908, 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?

findings reveal new roles for Six3 in eye development
Title: Six3 regulates optic nerve development via multiple mechanisms.
data find that Six3 promotes ventral telencephalic fates through transient regulation of foxg1a expression and repression of the Wnt/beta-catenin pathway.
Title: Six3 cooperates with Hedgehog signaling to specify ventral telencephalon by promoting early expression of Foxg1a and repressing Wnt signaling.
Study provides a comprehensive view of six3a transcription regulation during brain and eye development and offers an opportunity to establish the gene regulatory networks underlying neurogenesis in zebrafish.
Title: Complexity of cis-regulatory organization of six3a during forebrain and eye development in zebrafish.
the TAATGTC motif is an important target sequence for vertebrate Six3 proteins in vivo
Title: Autoregulatory binding sites in the zebrafish six3a promoter region define a new recognition sequence for Six3 proteins.
These results identify Six3 as a direct regulator of Shh expression and reveal a crossregulatory loop between Shh and Six3 in the ventral forebrain.
Title: Haploinsufficiency of Six3 fails to activate Sonic hedgehog expression in the ventral forebrain and causes holoprosencephaly.
Six3, a transcription factor essential for forebrain formation and associated with holoprosencephaly in humans, regulates diencephalic Nodal activity during initial establishment of brain asymmetry.
Title: Six3 represses nodal activity to establish early brain asymmetry in zebrafish.
Lhx2 may mediate an alternative or parallel pathway for control of cellular proliferation in the developing forebrain via Six3a.
Title: Lhx2 mediates the activity of Six3 in zebrafish forebrain growth.

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General gene information

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Markers

six3 (e-PCR)
- UniSTS:187034

fc10a08.x1 (e-PCR)
- UniSTS:192420

fc10a08.x1 (e-PCR)
- UniSTS:192421

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
involved_in eye development	IBA Inferred from Biological aspect of Ancestor more info
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

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 SIX3a

Names: etID309945.13; etID46760.13; sine oculis homeobox homolog 3a

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_131362.1 → NP_571437.1 homeobox protein SIX3a

See identical proteins and their annotated locations for NP_571437.1

Status: PROVISIONAL

Source sequence(s)

AF030280

UniProtKB/TrEMBL

O73708

Related

ENSDARP00000075254.4, ENSDART00000080808.5

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