Hoxc4 homeo box C4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hoxc4provided by RGD
Official Full Name: homeo box C4provided by RGD
Primary source: RGD:1586210
See related: EnsemblRapid:ENSRNOG00000016613 AllianceGenome:RGD:1586210
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
Also known as: Hox3r3
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; HMG box domain binding activity; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in cellular response to glial cell derived neurotrophic factor and positive regulation of male germ-line stem cell asymmetric division. Predicted to be located in nucleoplasm. Orthologous to human HOXC4 (homeobox C4). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 26.5), Uterus (RPKM 14.3) and 5 other tissues See more
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Genomic context

Location:: 7q36

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (136049059..136051601)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (134135279..134173133)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (144646605..144652589)

Chromosome 7 - NC_086025.1 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

Hoxc4 (e-PCR), detects polymorphism
- UniSTS:143389

HOX3A (e-PCR)
- UniSTS:266290

Hoxc4 (e-PCR), detects polymorphism
- UniSTS:536661

NoName (e-PCR)
- UniSTS:491379

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables HMG box domain binding	IEA Inferred from Electronic Annotation more info
enables HMG box domain binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region 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 anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
involved_in cartilage development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cartilage development	ISO Inferred from Sequence Orthology more info
involved_in cellular response to glial cell derived neurotrophic factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in embryonic organ morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic organ morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of male germ-line stem cell asymmetric division	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal system development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein Hox-C4

Names: Homeobox gene C4; homeobox protein R3

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.