Irx6 iroquois homeobox 6 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Irx6provided by RGD
Official Full Name: iroquois homeobox 6provided by RGD
Primary source: RGD:1564830
See related: EnsemblRapid:ENSRNOG00000011037 AllianceGenome:RGD:1564830
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
Also known as: RGD1564830
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in cell development; neuron differentiation; and regulation of DNA-templated transcription. Predicted to act upstream of or within detection of visible light; negative regulation of DNA-templated transcription; and retina morphogenesis in camera-type eye. Predicted to be active in nucleus. Orthologous to human IRX6 (iroquois homeobox 6). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 1.3), Kidney (RPKM 0.5) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19p11

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (30503416..30509396, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (14330440..14336403, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (15726633..15733442, complement)

Chromosome 19 - NC_086037.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription repressor 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

Process	Evidence Code	Pubs
involved_in cell development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within detection of visible light	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor 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 transcription by RNA polymerase II	IEA Inferred from Electronic Annotation 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 retina layer formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retinal bipolar neuron differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: iroquois-class homeodomain protein IRX-6

Names: Iroquois related homeobox 6

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_001102413.2 → NP_001095883.1 iroquois-class homeodomain protein IRX-6 isoform 1

See identical proteins and their annotated locations for NP_001095883.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000019

UniProtKB/TrEMBL

A6KD59, D4A7R4

Related

ENSRNOP00000014831.4, ENSRNOT00000014831.6

Conserved Domains (2) summary

COG5576
Location:142 → 222

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam05920
Location:161 → 200

Homeobox_KN; Homeobox KN domain
NM_001434430.1 → NP_001421359.1 iroquois-class homeodomain protein IRX-6 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000019

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_086037.1 Reference GRCr8

Range

30503416..30509396 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063278003.1 → XP_063134073.1 iroquois-class homeodomain protein IRX-6 isoform X2
XM_063278002.1 → XP_063134072.1 iroquois-class homeodomain protein IRX-6 isoform X1