Six1 SIX homeobox 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Six1provided by RGD
Official Full Name: SIX homeobox 1provided by RGD
Primary source: RGD:620906
See related: EnsemblRapid:ENSRNOG00000022777 AllianceGenome:RGD:620906
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 transcription coactivator binding activity. Involved in cellular response to 3,3',5-triiodo-L-thyronine. Predicted to be located in nucleolus and nucleoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. 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, Dec 2024]
Expression: Biased expression in Muscle (RPKM 314.9), Thymus (RPKM 30.5) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 6q24

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (97482617..97487853, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (91746739..91751975, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (95929060..95934296, complement)

Chromosome 6 - NC_086024.1 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: 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?

SIX1 induced HULC modulates neuropathic pain and Schwann cell oxidative stress after sciatic nerve injury.
Title: SIX1 induced HULC modulates neuropathic pain and Schwann cell oxidative stress after sciatic nerve injury.
SIX1 attenuates inflammation and rheumatoid arthritis by silencing MyD88-dependent TLR1/2 signaling.
Title: SIX1 attenuates inflammation and rheumatoid arthritis by silencing MyD88-dependent TLR1/2 signaling.
Downregulation of Eya1 and Six1 gene expression in nitrofen-induced PH suggests that decreased Eya1 and Six1 expression during the late pseudoglandular stage may interfere with epithelial branching and distal airway maturation, thus resulting in PH.
Title: Expression of Eya1 and Six1 is decreased in distal airways of rats with experimental pulmonary hypoplasia.

Submit: New GeneRIF Correction

General gene information

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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	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 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 chromatin 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 transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Notch signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within aorta morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within branching involved in ureteric bud morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to 3,3',5-triiodo-L-thyronine	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cochlea morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic skeletal system morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in endothelin receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epithelial cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within facial nerve morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in fungiform papilla morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in gene expression	ISO Inferred from Sequence Orthology more info
involved_in generation of neurons	ISO Inferred from Sequence Orthology more info
involved_in inner ear development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in kidney development	ISO Inferred from Sequence Orthology more info
acts_upstream_of mesenchymal cell proliferation involved in ureter development	ISO Inferred from Sequence Orthology more info
involved_in mesonephric tubule formation	ISO Inferred from Sequence Orthology more info
involved_in metanephric mesenchyme development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within middle ear morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within myoblast migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of myoblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in myotome development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in neural crest cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron fate specification	ISO Inferred from Sequence Orthology more info
involved_in olfactory placode formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within organ induction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within otic vesicle development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within outflow tract morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pattern specification process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pharyngeal system development	ISO Inferred from Sequence Orthology more info
involved_in pharyngeal system development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of branching involved in ureteric bud morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of branching involved in ureteric bud morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of brown fat cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of mesenchymal cell proliferation involved in ureter development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of myoblast proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of secondary heart field cardioblast proliferation	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
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ureteric bud formation	ISO Inferred from Sequence Orthology more info
involved_in protein localization to nucleus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of branch elongation involved in ureteric bud branching	ISO Inferred from Sequence Orthology more info
involved_in regulation of epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of protein localization	ISO Inferred from Sequence Orthology more info
involved_in regulation of skeletal muscle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of skeletal muscle cell proliferation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of skeletal muscle satellite cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of synaptic assembly at neuromuscular junction	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 sensory perception of sound	ISO Inferred from Sequence Orthology more info
involved_in skeletal muscle fiber development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within skeletal muscle tissue development	ISO Inferred from Sequence Orthology more info
involved_in skeletal muscle tissue development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal system morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within thymus development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within thyroid gland development	ISO Inferred from Sequence Orthology more info
involved_in tongue development	ISO Inferred from Sequence Orthology more info
involved_in trigeminal ganglion development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ureter smooth muscle cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ureteric bud development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
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
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: homeobox protein SIX1

Names: sine oculis homeobox homolog 1; sine oculis-related homeobox 1 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_053759.1 → NP_446211.1 homeobox protein SIX1

See identical proteins and their annotated locations for NP_446211.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/TrEMBL

A6HC52, G3V970, Q99P83

Related

ENSRNOP00000037345.4, ENSRNOT00000034338.6

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