Irx1 iroquois homeobox 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Irx1provided by RGD
Official Full Name: iroquois homeobox 1provided by RGD
Primary source: RGD:1309060
See related: Ensembl:ENSRNOG00000033609 AllianceGenome:RGD:1309060
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 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; negative regulation of transcription by RNA polymerase II; and neuron differentiation. Predicted to act upstream of or within proximal/distal pattern formation involved in metanephric nephron development and specification of loop of Henle identity. Predicted to be active in nucleus. Orthologous to human IRX1 (iroquois homeobox 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 74.0), Kidney (RPKM 51.2) and 3 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1p11

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (33123122..33128951)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (31294615..31300444)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (33910912..33916741)

Chromosome 1 - NC_086019.1 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?

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General gene information

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Markers

AI426466 (e-PCR)
- UniSTS:160319

RH136785 (e-PCR)
- UniSTS:218874

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor 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
enables molecular_function	ND No biological Data available 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 cell development	IBA Inferred from Biological aspect of Ancestor more info
involved_in metanephros development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proximal/distal pattern formation involved in metanephric nephron development	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 response to organic cyclic compound	IDA Inferred from Direct Assay more info	PubMed
involved_in specification of loop of Henle identity	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cellular_component	ND No biological Data available more info
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-1

Names: Iroquois related homeobox 1

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_001107331.2 → NP_001100801.1 iroquois-class homeodomain protein IRX-1

See identical proteins and their annotated locations for NP_001100801.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A6JUZ0, D4A9L1

Related

ENSRNOP00000040590.3, ENSRNOT00000044690.5

Conserved Domains (3) summary

smart00548
Location:309 → 326

IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function

pfam05285
Location:194 → 252

SDA1; SDA1

pfam05920
Location:145 → 184

Homeobox_KN; Homeobox KN 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_086019.1 Reference GRCr8

Range

33123122..33128951

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039110061.2 → XP_038965989.1 iroquois-class homeodomain protein IRX-1 isoform X1

Conserved Domains (3) summary

smart00548
Location:148 → 165

IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function

cl00084
Location:1 → 23

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.

cl01319
Location:27 → 86

HARE-HTH; HB1, ASXL, restriction endonuclease HTH domain