Six4 SIX homeobox 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Six4provided by RGD
Official Full Name: SIX homeobox 4provided by RGD
Primary source: RGD:1306726
See related: Ensembl:ENSRNOG00000007250 AllianceGenome:RGD:1306726
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: 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 animal organ development; positive regulation of morphogenesis of an epithelium; and regulation of transcription, DNA-templated. Predicted to act upstream of or within several processes, including animal organ development; myoblast migration; and regulation of synaptic assembly at neuromuscular junction. Predicted to be located in cytoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human SIX4 (SIX homeobox 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 136.7), Kidney (RPKM 22.5) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q24

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (97538202..97551872, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (91802328..91816002, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (95984868..95999709, complement)

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?

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General gene information

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Markers

RH129748 (e-PCR)
- UniSTS:213041

D50417 (e-PCR)
- UniSTS:124838

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 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
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 fungiform papilla morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in generation of neurons	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in male gonad development	ISO Inferred from Sequence Orthology more info
involved_in male sex determination	ISO Inferred from Sequence Orthology more info
involved_in male sex differentiation	ISO Inferred from Sequence Orthology more info
involved_in metanephric mesenchyme development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within myoblast migration	ISO Inferred from Sequence Orthology more info
involved_in myotome development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	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
involved_in negative regulation of satellite cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in olfactory placode formation	ISO Inferred from Sequence Orthology more info
involved_in pharyngeal system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	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
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 ureteric bud formation	ISO Inferred from Sequence Orthology more info
involved_in protein localization to nucleus	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 protein localization	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
involved_in sarcomere organization	ISO Inferred from Sequence Orthology more info
involved_in skeletal muscle fiber differentiation	ISO Inferred from Sequence Orthology 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 thymus 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

Component	Evidence Code	Pubs
located_in cytoplasm	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

General protein information

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Preferred Names: homeobox protein SIX4

Names: sine oculis-related homeobox 4 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_001106739.2 → NP_001100209.1 homeobox protein SIX4 isoform 3

See identical proteins and their annotated locations for NP_001100209.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/TrEMBL

A6HC53, D3ZAJ7

Related

ENSRNOP00000050667.2, ENSRNOT00000050138.3

Conserved Domains (2) summary

cd00086
Location:151 → 205

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:31 → 140

SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain
NM_001414919.1 → NP_001401848.1 homeobox protein SIX4 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006
NM_001414920.1 → NP_001401849.1 homeobox protein SIX4 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/TrEMBL

A0A8I6AM05

Related

ENSRNOP00000089936.1, ENSRNOT00000117601.1