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    HCFC2 host cell factor C2 [ Homo sapiens (human) ]

    Gene ID: 29915, updated on 28-Oct-2024

    Summary

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    Official Symbol
    HCFC2provided by HGNC
    Official Full Name
    host cell factor C2provided by HGNC
    Primary source
    HGNC:HGNC:24972
    See related
    Ensembl:ENSG00000111727 MIM:607926; AllianceGenome:HGNC:24972
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HCF2; HCF-2
    Summary
    This gene encodes one of two proteins which interact with VP16, a herpes simplex virus protein that initiates virus infection. Both the encoded protein and the original Herpes host cell factor interact with VP16 through a beta-propeller domain. The original Herpes host cell factor, however, is effective at initiating viral infection while the encoded protein is not. Transcripts of varying length due to alternative polyadenylation signals have been described. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in testis (RPKM 10.0), endometrium (RPKM 3.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HCFC2 in Genome Data Viewer
    Location:
    12q23.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (104064531..104106524)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (104026224..104068218)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (104458309..104500302)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6905 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23620 Neighboring gene thymine DNA glycosylase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23681 Neighboring gene glycosyltransferase 8 domain containing 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:104408145-104408367 Neighboring gene phosphoglycerate mutase 1 (brain) pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23711 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4784 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:104458005-104458174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4786 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23722 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23731 Neighboring gene RNA, 5S ribosomal pseudogene 370 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104530547-104531140 Neighboring gene nuclear transcription factor Y subunit beta Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104531141-104531732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4790 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23735 Neighboring gene uncharacterized LOC105369947

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Herpes simplex virus transactivator VP16 discriminates between HCF-1 and a novel family member, HCF-2. Johnson KM, et al. J Virol, 1999 May. PMID 10196288, Free PMC Article
    2. HCF-2 inhibits cell proliferation and activates differentiation-gene expression programs. Gudkova D, et al. Nucleic Acids Res, 2019 Jun 20. PMID 31049581, Free PMC Article
    3. Host cell factors stimulate HIV-1 transcription by antagonizing substrate-binding function of Siah1 ubiquitin ligase to stabilize transcription elongation factor ELL2. Wu J, et al. Nucleic Acids Res, 2020 Jul 27. PMID 32479599, Free PMC Article
    4. Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Park SH, et al. Nat Commun, 2019 Dec 5. PMID 31804488, Free PMC Article
    5. Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. Yokoyama A, et al. Mol Cell Biol, 2004 Jul. PMID 15199122, Free PMC Article

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HCF-2 is broadly present in human and mouse cells, and possesses activities distinct from HCF-1
      Title: HCF-2 inhibits cell proliferation and activates differentiation-gene expression programs.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ94012

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in antiviral innate immune response IEA
    Inferred from Electronic Annotation
    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
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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
    		  
    involved_in regulation of transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in viral process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of MLL1 complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of MLL1/2 complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of Set1C/COMPASS complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    part_of histone methyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    host cell factor 2
    Names
    C2 factor

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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)

    1. NM_013320.3 → NP_037452.1  host cell factor 2

      See identical proteins and their annotated locations for NP_037452.1

      Status: REVIEWED

      Source sequence(s)
      AC089983, AI247087, BC033799, DB030069
      Consensus CDS
      CCDS9097.1
      UniProtKB/Swiss-Prot
      B2R8Q5, C0H5X3, Q9Y5Z7
      UniProtKB/TrEMBL
      Q53FE7
      Related
      ENSP00000229330.4, ENST00000229330.9
      Conserved Domains (5) summary
      PLN02193
      Location:2 → 262
      PLN02193; nitrile-specifier protein
      cd00063
      Location:618 → 672
      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]
      pfam13415
      Location:207 → 253
      Kelch_3; Galactose oxidase, central domain
      pfam13854
      Location:312 → 354
      Kelch_5; Kelch motif

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      104064531..104106524
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428753.1 → XP_047284709.1  host cell factor 2 isoform X2

    2. XM_017019242.3 → XP_016874731.1  host cell factor 2 isoform X1

    3. XM_047428754.1 → XP_047284710.1  host cell factor 2 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      104026224..104068218
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371893.1 → XP_054227868.1  host cell factor 2 isoform X2

    2. XM_054371892.1 → XP_054227867.1  host cell factor 2 isoform X1

    3. XM_054371894.1 → XP_054227869.1  host cell factor 2 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5Z7.1 GenPept UniProtKB/Swiss-Prot:Q9Y5Z7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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