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HCP5 Gene

RNA gene   GIFtS: 39
GCID: GC06P031375

HLA Complex P5 (Non-Protein Coding)

(Previous name: HLA complex P5)
Microbiology & Infectious Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 3

Aliases
HLA Complex P5 (Non-Protein Coding)1 2     P5-12
6S2650E2 5     HLA Complex Protein P53
HLA Complex P51     Protein P5-13
D6S2650E2     

External Ids:    HGNC: 216591   Entrez Gene: 108662   Ensembl: ENSG000002063377   OMIM: 6046765   UniProtKB: Q6MZN73   
ORGUL members:         

Export aliases for HCP5 gene to outside databases

Previous GC identifers: GC06P031201 GC06P031535 GC06P031538 GC01M241088 GC06P031430 GC06Pj31419 GC06P031372


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for HCP5 Gene:
HCP5 (HLA complex P5 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with HCP5 include abacavir hypersensitivity, and drug-induced liver injury due to flucloxacillin.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the HCP5 gene promoter:
         AhR   Egr-1   Pax-2   Pax-2a   Arnt   Egr-4   AREB6   c-Rel   Ik-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHCP5 promoter sequence
   Search Chromatin IP Primers for HCP5

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HCP5


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p21.33   HGNC cytogenetic band: 6p21.3

HCP5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HCP5 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P031375:  view genomic region     (about GC identifiers)

Start:
31,368,479 bp from pter      End:
31,445,283 bp from pter
Size:
76,805 bases      Orientation:
plus strand

2 alternative locations:
Chr6+,NT_113891.2 2,940,611-2,943,240      Chr6+,NT_167249 2,761,727-2,764,356     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: HCP5_HUMAN, Q6MZN7 (See protein sequence)
Recommended Name: HLA class I histocompatibility antigen protein P5  
Size: 132 amino acids; 14098 Da
Miscellaneous: Variation Gly-112 is associated with low viral loads in untreated HIV patients. The level of
circulating virus in the plasma of HIV patients (viral set point) varies among individuals during the
nonsymptomatic phase preceding the progression to AIDS. This polymorphism explains 9.6% of the total variation in
set point and is associated with the HLA-B*5701 allele, which has the strongest described protective impact on
HIV disease progression. However, it is possible that HPC5 polymorphism, and not HLA-B*5701 allele, plays a
direct role in the control in viremia in HIV patients
Miscellaneous: HCP5 is localized within the MHC class I region, but is not structurally related to MHC class I
genes. HCP5 is related in sequence to human endogenous retroviruses HERV-L and HERV-16. It has sequence homology
with retroviral Pol genes in HERV retroviral element; thus, it is itself a good candidate to interact with HIV-1,
possibly through an antisense mechanism against retroviral transcript
Sequence caution: Sequence=AAA59986.1; Type=Frameshift; Positions=58, 125;
Secondary accessions: Q04490

Explore the universe of human proteins at neXtProt for HCP5: NX_Q6MZN7

Explore proteomics data for HCP5 at MOPED


See HCP5 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

ProtoNet protein and cluster: Q6MZN7


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HCP5
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HCP5
Interactions:

    Search GeneGlobe Interaction Network for HCP5

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006952defense response TAS8462994

HCP5 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for HCP5



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000414046(sense_overlapping) ENST00000460889(sense_overlapping) ENST00000467369(sense_overlapping) ENST00000541196(sense_overlapping)
Congresses - knowledge worth sharing:
European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

miRNA
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Search for qRT-PCR Assays for microRNAs that regulate HCP5
SwitchGear 3'UTR luciferase reporter plasmidHCP5 3' UTR sequence
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  QuantiTect SYBR Green Assays in human, mouse, rat HCP5
  QuantiFast Probe-based Assays in human, mouse, rat HCP5

Selected AceView cDNA sequences (see all 109):

AL555668 AA313338 AI282556 CR626077 BM836915 BQ925322 AI911613 AJ437509 
T28905 AA642585 BU620516 BU687810 BU529025 NM_006674 BQ935363 AW188708 
AK093953 AA890242 AI872340 BU623002 AI624797 BX640979 AA149082 BQ943852 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for HCP5:none

HCP5 expression in normal human tissues (normalized intensities)      HCP5 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ATGTTGTCAA
HCP5 Expression
About this image


HCP5 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 3) fully expand
 
 Thymus (Hematopoietic System)    fully expand to see all 2 entries
         T Helper Cells Thymus
 
 Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
         Human embryonic stem cells (family)
 
 Blood (Cardiovascular System)    fully expand to see all 2 entries
         T Helper Cells Thymus
HCP5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

HCP5 Protein Expression

UniProtKB/Swiss-Prot: HCP5_HUMAN, Q6MZN7
Tissue specificity: Expressed in lymphoid tissues; Detected in spleen as well as in B-cell lines, NK cell lines
and activated lymphocytes

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QuantiFast Probe-based Assays in human, mouse, rat HCP5
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HCP5

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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ENSEMBL Gene Tree for HCP5 (if available)
TreeFam Gene Tree for HCP5 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for HCP5 (see all 150)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs25964721,2
C,F,A,H--31428967(+) aagcCA/GTAATG 1 -- us2k129Minor allele frequency- G:0.18NS EA NA WA CSA 2846
rs773492731,2
C,F--31428987(+) CATTGC/TTATTT 1 -- us2k11Minor allele frequency- T:0.16NA 120
rs1846920151,2
--31429113(+) GGCTCA/TCATTT 1 -- us2k10--------
rs1891418791,2
--31429119(+) CATTTA/GTAATT 1 -- us2k10--------
rs796396021,2
C--31429228(+) TTAAAA/CATTAG 1 -- us2k10--------
rs1817512201,2
--31429239(+) TCAGCC/TATGGT 1 -- us2k10--------
rs1172980431,2
F--31429286(+) GAGGCG/AGAAGG 1 -- us2k11Minor allele frequency- A:0.02EA 120
rs1125006591,2
C--31429296(+) GATCAG/CTTGAG 1 -- us2k11Minor allele frequency- C:0.50CSA 2
rs1466443461,2
--31429403(+) AAATAA/GATAGA 1 -- us2k10--------
rs1868281771,2
--31429410(+) TAGAAA/GTTATA 1 -- us2k10--------

HapMap Linkage Disequilibrium report for HCP5 (31368479 - 31445283 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for HCP5 (see all 36):    About this table    
Variant IDTypeSubtypePubMed ID
esv2432528CNV Deletion19546169
esv2731822CNV Deletion23290073
dgv1098e199CNV Deletion23128226
nsv435829CNV Deletion17901297
dgv1042e201CNV Deletion23290073
esv3160CNV Duplication18987735
nsv513736CNV Insertion21212237
nsv818409CNV Loss17921354
nsv5246CNV Loss18451855
nsv884405CNV Loss21882294

Human Gene Mutation Database (HGMD): HCP5
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing HCP5
DNA2.0 Custom Variant and Variant Library Synthesis for HCP5

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 604676    OMIM disorders: --

12 diseases for HCP5:    About MalaCards
abacavir hypersensitivity    drug-induced liver injury due to flucloxacillin    toxic epidermal necrolysis    stevens-johnson syndrome
psoriatic arthritis    hypothyroidism    urticaria    hiv-1
psoriasis    systemic lupus erythematosus    lupus erythematosus    arthritis


HCP5 for disorders           About GeneDecksing


Congresses - knowledge worth sharing:
The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014
Genetic Association Database (GAD): HCP5
Human Genome Epidemiology (HuGE) Navigator: HCP5 (15 documents)

Export disorders for HCP5 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for HCP5 gene, integrated from 10 sources (see all 33):
(articles sorted by number of sources associating them with HCP5)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The P5 multicopy gene family in the MHC is related in sequence to human endogenous retroviruses HERV-L and HERV-16. (PubMed id 10199916)1, 2, 3 Kulski J.K. and Dawkins R.L. (Immunogenetics 1999)
  2. A novel coding sequence belonging to a new multicopy gene family mapping within the human MHC class I region. (PubMed id 8462994)1, 2, 3 Vernet C....Pontarotti P. (Immunogenetics 1993)
  3. Use of the HCP5 single nucleotide polymorphism to predict hypersensitivity reactions to abacavir: correlation with HLA-B*5701. (PubMed id 20534626)1, 4 RodrA-guez-NA^voa S....Soriano V. (J. Antimicrob. Chemother. 2010)
  4. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. (PubMed id 21051598)1, 4  ....Zhao M. (Science 2010)
  5. Common genetic variation and the control of HIV-1 in humans. (PubMed id 20041166)1, 4 Fellay J....Goldstein D.B. (PLoS Genet. 2009)
  6. Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). (PubMed id 19115949)1, 4 Limou S....Zagury J.F. (J. Infect. Dis. 2009)
  7. HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. (PubMed id 19483685)1, 4 Daly A.K.... . (Nat. Genet. 2009)
  8. Association of HLA-C and HCP5 gene regions with the clinical course of HIV-1 infection. (PubMed id 19050382)1, 4 van Manen D....Schuitemaker H. (AIDS 2009)
  9. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1, 4 Barcellos L.F....Criswell L.A. (PLoS Genet. 2009)
  10. A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. (PubMed id 18369459)1, 4 Liu Y....Bowcock A.M. (PLoS Genet. 2008)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 10866 HGNC: 21659 AceView: HCP5 Ensembl:ENSG00000206337 euGenes: HUgn10866
ECgene: HCP5 H-InvDB: HCP5

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for HCP5 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for HCP5 gene:
Search GeneIP for patents involving HCP5

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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