Hcfc2 host cell factor C2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hcfc2provided by RGD
Official Full Name: host cell factor C2provided by RGD
Primary source: RGD:1307385
See related: EnsemblRapid:ENSRNOG00000053510 AllianceGenome:RGD:1307385
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 transcription coactivator activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in cytosol; nuclear body; and plasma membrane. Predicted to be part of MLL1 complex and Set1C/COMPASS complex. Orthologous to human HCFC2 (host cell factor C2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 138.8), Heart (RPKM 114.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q13

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (22875440..22907391, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (20983986..21019826, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (27107931..27136658, complement)

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 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

AW435314 (e-PCR)
- UniSTS:249053

AI008665 (e-PCR)
- UniSTS:250610

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coregulator activity	IEA Inferred from Electronic Annotation more info
enables transcription coregulator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in antiviral innate immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within antiviral innate immune response	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in immune response involved in response to exogenous dsRNA	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within immune response involved in response to exogenous dsRNA	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of toll-like receptor 3 signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of toll-like receptor 3 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of MLL1 complex	IEA Inferred from Electronic Annotation more info
part_of MLL1 complex	ISO Inferred from Sequence Orthology more info
part_of MLL1/2 complex	ISO Inferred from Sequence Orthology more info
part_of Set1C/COMPASS complex	IEA Inferred from Electronic Annotation more info
part_of Set1C/COMPASS complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
part_of histone methyltransferase complex	IBA Inferred from Biological aspect of Ancestor more info
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: host cell factor 2

Names: C2 factor; HCF-2

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_001008357.1 → NP_001008358.1 host cell factor 2

See identical proteins and their annotated locations for NP_001008358.1

Status: PROVISIONAL

Source sequence(s)

BC085951

UniProtKB/Swiss-Prot

Q5RKG2

UniProtKB/TrEMBL

A0A0G2JXF9, A6IFI3

Related

ENSRNOP00000070255.2, ENSRNOT00000086905.3

Conserved Domains (6) summary

PLN02193
Location:2 → 262

PLN02193; nitrile-specifier protein

cd00063
Location:549 → 603

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

sd00038
Location:190 → 241

Kelch; KELCH repeat [structural motif]

pfam01344
Location:22 → 59

Kelch_1; Kelch motif

pfam13415
Location:207 → 253

Kelch_3; Galactose oxidase, central domain

pfam13854
Location:312 → 354

Kelch_5; Kelch motif

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_086025.1 Reference GRCr8

Range

22875440..22907391 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039079037.2 → XP_038934965.1 host cell factor 2 isoform X1

UniProtKB/TrEMBL

A0A0G2JXF9, A0A8I5Y755

Related

ENSRNOP00000104880.1, ENSRNOT00000147485.1

Conserved Domains (2) summary

PLN02193
Location:2 → 262

PLN02193; nitrile-specifier protein

sd00038
Location:190 → 241

Kelch; KELCH repeat [structural motif]
XM_039079039.2 → XP_038934967.1 host cell factor 2 isoform X2

Conserved Domains (2) summary

PLN02193
Location:2 → 262

PLN02193; nitrile-specifier protein

sd00038
Location:190 → 241

Kelch; KELCH repeat [structural motif]