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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HCP5 Gene

RNA gene   GIFtS: 42
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)
About This Section

Subcategory (RNA class): sense_overlapping

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   

Export aliases for HCP5 gene to outside databases

Previous GC identifers: GC06P031201 GC06P031535 GC06P031538 GC01M241088 GC06P031430 GC06Pj31419 GC06P031372


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for HCP5 Gene: 
HCP5 (HLA complex P5 (non-protein coding)) is an RNA gene, and is affiliated with the sense_overlapping RNA class. Diseases associated with HCP5 include toxic epidermal necrolysis, and psoriatic arthritis.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.2  NT_007592.15  NT_113891.2  NT_167247.1  NT_167249.1  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for HCP5

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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 

HCP5 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

HCP5 Protein Expression

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
   inGenious Targeting Laboratory - Custom generated mouse model solutions for HCP5 
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miRNA
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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HCP5

Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    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 HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for HCP5

Search CenterWatch for drugs/clinical trials and news about 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,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

Unigene Cluster for HCP5:

HLA complex P5 (non-protein coding)
Hs.691948  [show with all ESTs]
Unigene Representative Sequence: NR_040662
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 QIAGEN for miScript miRNA Assays for microRNAs that regulate HCP5
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Inhib. RNA
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DNA2.0 Custom Codon Optimized Gene Synthesis Service for HCP5
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HCP5
Sirion Biotech Customized lentivirus for stable overexpression of HCP5 
                     Customized lentivirus expression plasmids for stable overexpression of HCP5 
Primer
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OriGene qPCR primer pairs and template standards for HCP5
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  QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HCP5
  QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HCP5

Additional mRNA sequence: 

AJ437509.2 AK093953.1 AK290875.1 BC106759.2 BC113853.1 BC114462.1 BX640979.1 L06175.1 
L29367.1 NR_040662.1 

10 DOTS entries:

DT.97768739  DT.313725  DT.100688520  DT.92422376  DT.100688519  DT.92070423  DT.100020361  DT.100866984 
DT.95340351  DT.95272356 

24/109 AceView cDNA sequences (see all 109):

CR626077 AJ437509 AA642585 BE326777 AA313338 BU687810 AI889617 AI282556 
BU620516 BU623002 BX640979 BQ943852 BM836915 AL555668 AA890242 BQ925322 
AA149082 AW188708 AI911613 NM_006674 AK093953 AI872340 AA805255 BU528920 

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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

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 
 5/5 selected tissues (see all 5) fully expand
 
 Thymus (Hematopoietic System)    fully expand to see all 2 entries
         T Helper Cells Thymus
 
 Blood (Cardiovascular System)    fully expand to see all 2 entries
         T Helper Cells Thymus
 
 Inner Cell Mass (Early Embryonic Tissues)
         Line H9 (WA09)
 
 Uterus (Reproductive System)
         CERVIX   
 
 Lymph (Hematopoietic System)
         LYMPH NODE   

See HCP5 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for HCP5

SOURCE GeneReport for Unigene cluster: Hs.691948

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

    SABiosciences Custom PCR Arrays for HCP5
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QIAGEN 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)
About This Section
  --

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)
About This Section
  --

(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/150 SNPs in HCP5 are shown (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) 10/36 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
SABiosciences Cancer Mutation 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.)
About This Section
OMIM gene information: 604676    OMIM disorders: --

8 diseases for HCP5:    About MalaCards
toxic epidermal necrolysis    psoriatic arthritis    stevens-johnson syndrome    hypothyroidism
psoriasis    systemic lupus erythematosus    lupus erythematosus    arthritis


HCP5 for disorders           About GeneDecksing

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)
About This Section

PubMed articles for HCP5 gene, integrated from 9 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. (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. (1993)
  3. Use of the HCP5 single nucleotide polymorphism to pre dict hypersensitivity reactions to abacavir: correlation with HLA-B*5701. (PubMed id 20534626)1, 4 RodrA-guez-NA^voa S....Soriano V. (2010)
  4. The major genetic determinants of HIV-1 control affec t HLA class I peptide presentation. (PubMed id 21051598)1, 4  ....Zhao M. (2010)
  5. Common genetic variation and the control of HIV-1 in humans. (PubMed id 20041166)1, 4 Fellay J....Goldstein D.B. (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. (2009)
  7. HLA-B*5701 genotype is a major determinant of drug-in duced liver injury due to flucloxacillin. (PubMed id 19483685)1, 4 Daly A.K....Day C.P. (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. (2009)
  9. High-density SNP screening of the major histocompatib ility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1, 4 Barcellos L.F....Criswell L.A. (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. (2008)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 10866 HGNC: 21659 AceView: HCP5 Ensembl:ENSG00000206337 euGenes: HUgn10866
ECgene: HCP5 H-InvDB: HCP5

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
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.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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 Proteins for HCP5
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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transforming growth factor, beta 1
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The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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