Human Gene HCFC2 (uc001tkj.4) Description and Page Index
  Description: Homo sapiens host cell factor C2 (HCFC2), mRNA.
RefSeq Summary (NM_013320): 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]. ##Evidence-Data-START## Transcript exon combination :: SRR1803612.206310.1, SRR1660803.229480.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000229330.9/ ENSP00000229330.4 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr12:104,458,236-104,500,304 Size: 42,069 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr12:104,458,339-104,497,051 Size: 38,713 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:104,458,236-104,500,304)mRNA (may differ from genome)Protein (792 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: HCFC2_HUMAN
DESCRIPTION: RecName: Full=Host cell factor 2; Short=HCF-2; AltName: Full=C2 factor;
SUBUNIT: Binds MLL. Component of the MLL1/MLL complex, at least composed of MLL, ASH2L, RBBP5, DPY30, WDR5, MEN1, HCFC1 and HCFC2.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Highly expressed in testis. Detected at lower levels in spleen, thymus, prostate, ovary, small intestine and colon.
SIMILARITY: Contains 3 fibronectin type-III domains.
SIMILARITY: Contains 4 Kelch repeats.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HCFC2
CDC HuGE Published Literature: HCFC2
Positive Disease Associations: Heart Failure
Related Studies:
  1. Heart Failure
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: HCFC2
Diseases sorted by gene-association score: herpes simplex (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 16.73 RPKM in Testis
Total median expression: 204.80 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -48.20103-0.468 Picture PostScript Text
3' UTR -754.893253-0.232 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003961 - Fibronectin_type3
IPR013783 - Ig-like_fold
IPR015915 - Kelch-typ_b-propeller

Pfam Domains:
PF01344 - Kelch motif
PF13415 - Galactose oxidase, central domain
PF13854 - Kelch motif

SCOP Domains:
49265 - Fibronectin type III
50965 - Galactose oxidase, central domain

ModBase Predicted Comparative 3D Structure on Q9Y5Z7
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGD  WormBase 
 Protein Sequence  Protein Sequence 
 Alignment  Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003713 transcription coactivator activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0016032 viral process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0071339 MLL1 complex


-  Descriptions from all associated GenBank mRNAs
  AK313466 - Homo sapiens cDNA, FLJ94012, Homo sapiens host cell factor 2 (HCF-2), mRNA.
AK223342 - Homo sapiens mRNA for host cell factor C2 variant, clone: TST01027.
BC006558 - Homo sapiens host cell factor C2, mRNA (cDNA clone MGC:2754 IMAGE:2823984), complete cds.
AF117210 - Homo sapiens host cell factor 2 (HCF-2) mRNA, complete cds.
BC033799 - Homo sapiens host cell factor C2, mRNA (cDNA clone MGC:45151 IMAGE:5172046), complete cds.
KJ902517 - Synthetic construct Homo sapiens clone ccsbBroadEn_11911 HCFC2 gene, encodes complete protein.
KJ898744 - Synthetic construct Homo sapiens clone ccsbBroadEn_08138 HCFC2 gene, encodes complete protein.
EU446491 - Synthetic construct Homo sapiens clone IMAGE:100069838; IMAGE:100011700; FLH258623.01L host cell factor C2 (HCFC2) gene, encodes complete protein.
AK296523 - Homo sapiens cDNA FLJ58092 complete cds, highly similar to Host cell factor 2.
JD244758 - Sequence 225782 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2R8Q5, HCFC2_HUMAN, NM_013320, NP_037452, Q9Y5Z7
UCSC ID: uc001tkj.4
RefSeq Accession: NM_013320
Protein: Q9Y5Z7 (aka HCFC2_HUMAN)
CCDS: CCDS9097.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_013320.2
exon count: 15CDS single in 3' UTR: no RNA size: 5743
ORF size: 2379CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4958.00frame shift in genome: no % Coverage: 99.86
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.