Six2 SIX homeobox 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Six2provided by RGD
Official Full Name: SIX homeobox 2provided by RGD
Primary source: RGD:1310792
See related: EnsemblRapid:ENSRNOG00000085124 AllianceGenome:RGD:1310792
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including embryonic morphogenesis; kidney development; and positive regulation of chondrocyte proliferation. Predicted to act upstream of or within several processes, including chondrocyte differentiation; condensed mesenchymal cell proliferation; and embryonic organ morphogenesis. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in renal Wilms' tumor. Orthologous to human SIX2 (SIX homeobox 2). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Muscle (RPKM 35.2) and Thymus (RPKM 24.7) See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

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 (14727756..14734219)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (8974859..8981345)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (8952572..8955893, complement)

Chromosome 6 - NC_086024.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Markers

Six2 (e-PCR), detects polymorphism
- UniSTS:547307

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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 protein-containing complex 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

Process	Evidence Code	Pubs
involved_in anterior/posterior axis specification	ISO Inferred from Sequence Orthology more info
involved_in cell migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within condensed mesenchymal cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic digestive tract morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic skeletal system morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of epithelial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in kidney development	IBA Inferred from Biological aspect of Ancestor more info
involved_in kidney development	ISO Inferred from Sequence Orthology more info
involved_in mesenchymal cell differentiation involved in kidney development	ISO Inferred from Sequence Orthology more info
involved_in mesenchymal stem cell maintenance involved in nephron morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in mesenchymal stem cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in mesodermal cell fate specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within metanephros 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 negative regulation of epithelial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in nephron development	ISO Inferred from Sequence Orthology more info
involved_in nephron morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of chondrocyte 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
acts_upstream_of_or_within protein import into nucleus	ISO Inferred from Sequence Orthology more info
involved_in regulation of branching involved in ureteric bud morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of ossification	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

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

Go to the top of the page Help

Preferred Names: homeobox protein SIX2

Names: sine oculis-related homeobox 2 homolog

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001191908.1 → NP_001178837.1 homeobox protein SIX2

See identical proteins and their annotated locations for NP_001178837.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000006

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086024.1 Reference GRCr8

Range

14727756..14734219

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039112617.2 → XP_038968545.1 homeobox protein SIX2 isoform X2

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
XM_039112616.2 → XP_038968544.1 homeobox protein SIX2 isoform X1

UniProtKB/TrEMBL

A0A8I6ADX8

Related

ENSRNOP00000102713.1, ENSRNOT00000141758.1

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