Six3 SIX homeobox 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Six3provided by RGD
Official Full Name: SIX homeobox 3provided by RGD
Primary source: RGD:620909
See related: AllianceGenome:RGD:620909
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables signaling receptor binding activity. Involved in negative regulation of transcription, DNA-templated. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. 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]
Expression: Restricted expression toward (RPKM 2.2) See more
Orthologs: human mouse all
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Genomic context

Location:: 6q12

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (14791937..14796365, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (9039017..9043336, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (8886730..8891094)

Chromosome 6 - NC_086024.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Regulation of the AMPK/mTOR Axis Mitigates Tendon Stem/Progenitor Cell Senescence and Delays Tendon Aging.
Title: The Regulation of the AMPK/mTOR Axis Mitigates Tendon Stem/Progenitor Cell Senescence and Delays Tendon Aging.

Submit: New GeneRIF Correction

General gene information

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Markers

RH138952 (e-PCR)
- UniSTS:221038

Six3 (e-PCR), detects polymorphism
- UniSTS:536466

RH143896 (e-PCR)
- UniSTS:233142

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables signaling receptor binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription corepressor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in apoptotic process involved in development	ISO Inferred from Sequence Orthology more info
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within brain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within camera-type eye development	ISO Inferred from Sequence Orthology more info
involved_in cell proliferation in forebrain	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within circadian behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within diencephalon development	ISO Inferred from Sequence Orthology more info
involved_in epithelial cell maturation	ISO Inferred from Sequence Orthology more info
involved_in eye development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within eye development	ISO Inferred from Sequence Orthology more info
involved_in eye development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
involved_in forebrain dorsal/ventral pattern formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gonad development	ISO Inferred from Sequence Orthology more info
involved_in lens development in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in lens fiber cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in lens fiber cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lens induction in camera-type eye	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in neuroblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in neuroblast migration	ISO Inferred from Sequence Orthology more info
involved_in optic vesicle morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pituitary gland development	ISO Inferred from Sequence Orthology more info
involved_in pituitary gland development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein import into nucleus	ISO Inferred from Sequence Orthology more info
involved_in proximal/distal axis specification	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell cycle phase transition	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of neural precursor cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of neural retina development	ISO Inferred from Sequence Orthology more info
involved_in regulation of neuroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within telencephalon development	ISO Inferred from Sequence Orthology more info
involved_in telencephalon development	ISO Inferred from Sequence Orthology more info
involved_in telencephalon regionalization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within thyroid gland development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology 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 SIX3

Names: sine oculis homeobox homolog 3; sine oculis-related homeobox 3 homolog

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_023990.2 → NP_076480.1 homeobox protein SIX3

See identical proteins and their annotated locations for NP_076480.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/TrEMBL

A0A0G2K2C0, Q9ET75

Conserved Domains (2) summary

cd00086
Location:213 → 261

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:92 → 205

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