Hoxc9 homeobox C9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hoxc9provided by RGD
Official Full Name: homeobox C9provided by RGD
Primary source: RGD:1595784
See related: EnsemblRapid:ENSRNOG00000016199 AllianceGenome:RGD:1595784
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: Hoxc8
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within anterior/posterior pattern specification and embryonic skeletal system morphogenesis. Predicted to be located in aggresome and nucleoplasm. Predicted to be part of transcription repressor complex. Predicted to be active in nucleus. Orthologous to human HOXC9 (homeobox C9). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Muscle (RPKM 26.3), Kidney (RPKM 18.3) and 3 other tissues See more
Orthologs: human mouse all
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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 (135997292..135999969)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (134118817..134121497)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (144592462..144598807)

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?

The membrane attack complex of complement induces caspase activation and apoptosis.
Title: The membrane attack complex of complement induces caspase activation and apoptosis.

Submit: New GeneRIF Correction

General gene information

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Markers

Hoxc8 (e-PCR), detects polymorphism
- UniSTS:143391

Hoxc9 (e-PCR), detects polymorphism
- UniSTS:143392

MARC_41665-41666:1086710236:1 (e-PCR)
- UniSTS:471605

PMC15172P2 (e-PCR)
- UniSTS:271172

MARC_44775-44776:1100041323:1 (e-PCR)
- UniSTS:471623

Hoxc9 (e-PCR), detects polymorphism
- UniSTS:536665

MARC_46193-46194:1108499233:1 (e-PCR)
- UniSTS:471644

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 RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic skeletal system development	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 regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in aggresome	IEA Inferred from Electronic Annotation more info
located_in aggresome	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of transcription repressor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: homeobox protein Hox-C9

Names: homeo box C9

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.