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HCG22 Gene

RNA gene   GIFtS: 32
GCID: GC06P031022

HLA Complex Group 22

(Previous name: HLA complex group 22 (non-protein coding))
  See HCG22-related disease
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 Group 221 2 3
PBMUCL22 3 5
HLA Complex Group 22 (Non-Protein Coding)1
Panbronchiolitis Related Mucin-Like 21
G23
Panbronchiolitis-Related Mucin-Like Protein 23

External Ids:    HGNC: 277801   Entrez Gene: 2858342   Ensembl: ENSG000002287897   OMIM: 6139185   UniProtKB: E2RYF73   
ORGUL members:         

Export aliases for HCG22 gene to outside databases

Previous GC identifers: GC06U900708 GC06P031129 GC06Pf31157


(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 HCG22 Gene:
HCG22 (HLA complex group 22) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with HCG22 include follicular lymphoma.


(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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RefSeq DNA sequence at NCBI GenBank:
NC_000006.11  NC_018917.2  NT_007592.16  NT_113891.3  NT_167244.2  NT_167245.2  NT_167246.2  NT_167247.2  
NT_167248.2  NT_167249.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the HCG22 gene promoter:
         COUP-TF1   COUP   HNF-4alpha2   HNF-4alpha1   PPAR-gamma1   COUP-TF   Zic1   PPAR-gamma2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for HCG22

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HCG22


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

Entrez Gene cytogenetic band: 6p21.33   Ensembl cytogenetic band:  6p21.33   HGNC cytogenetic band: 6p21.32

HCG22 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HCG22 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P031022:  view genomic region     (about GC identifiers)

Start:
31,021,227 bp from pter      End:
31,027,667 bp from pter
Size:
6,441 bases      Orientation:
plus strand

Selected alternative locations (see all 7):
Chr6+,NT_167245 2,319,163-2,324,833      Chr6+,NT_167247 2,403,917-2,409,577      Chr6+,NT_167248 2,318,135-2,323,435     
Chr6+,NT_113891.2 2,536,690-2,542,360      Chr6+,NT_167246 2,370,339-2,376,003      Chr6+,NT_167249 2,356,966-2,362,624     
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for HCG22

(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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PBMU2_HUMAN, E2RYF7 (See protein sequence)
Recommended Name: Protein PBMUCL2 precursor  
Size: 251 amino acids; 26282 Da

Explore the universe of human proteins at neXtProt for HCG22: NX_E2RYF7

Post-translational modifications: 

  • Glycosylation2 at Asn120

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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: E2RYF7


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
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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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    Subcellular locations from UniProtKB/Swiss-Prot
    PBMU2_HUMAN, E2RYF7: Secreted (Potential)

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    Find genes that share ontologies with HCG22           About GenesLikeMe


    (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 HCG22
    Interactions:

        Search GeneGlobe Interaction Network for HCG22

    (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 HCG22 (PBMU2)



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    Unigene Cluster for HCG22:

    HLA complex group 22 (non-protein coding)
    Hs.207528  [show with all ESTs]
    Unigene Representative Sequence: NR_003948
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000565192(lincRNA)(uc021yui.1) ENST00000562344(lincRNA) ENST00000570223(lincRNA) ENST00000566475(lincRNA)
    ENST00000426185(lincRNA)(uc003nsj.2)
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    Additional mRNA sequence: 

    AB560771.1 AB600644.1 AK094433.1 NR_003948.2 

    1 DOTS entry:

    DT.99999057 

    3 AceView cDNA sequences:

    AK094433 AI804667 BM453661 

    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 HCG22:none

    HCG22 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGGAGGACAC
    HCG22 Expression
    About this image

    HCG22 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

    SOURCE GeneReport for Unigene cluster: Hs.207528

    UniProtKB/Swiss-Prot: PBMU2_HUMAN, E2RYF7
    Tissue specificity: Detected in the brain, lung, spleen, thymus and prostate

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    In Situ
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    (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 HCG22 (if available)
    TreeFam Gene Tree for HCG22 (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 HCG22 (see all 276)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs720217301,2
    C--30823776(+) AGAGA-/AAGAGAA 1 -- us2k10--------
    rs1118004741,2
    C--30823777(+) GAGAA-/AGAGAAA 1 -- us2k11Minor allele frequency- AG:0.00CSA 2
    rs25238611,2
    C,F,A,H--31019215(-) caacaG/Agtgtg 1 -- us2k111Minor allele frequency- A:0.43NA WA CSA EA 256
    rs92959461,2
    C--31019409(+) agctaC/Attgta 1 -- us2k14Minor allele frequency- A:0.08NA WA EA 360
    rs1180234411,2
    F--31019459(+) GAGGCT/AGTATG 1 -- us2k11Minor allele frequency- A:0.03EA 120
    rs92959471,2
    C,F,H--31019460(+) aggctG/Atatga 1 -- us2k116Minor allele frequency- A:0.11NS EA NA WA 2332
    rs354029471,2
    C--31019471(+) TGCCA-/CCTGCA 1 -- us2k10--------
    rs25238591,2
    C,F,A--31019475(-) attgcG/Agtggc 1 -- us2k111Minor allele frequency- A:0.44NA WA CSA EA 372
    rs1123747231,2
    C--31019478(+) ACTGCC/AATTCA 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs1922606161,2
    --31019494(+) GGAAAC/TGCAGT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for HCG22 (31021227 - 31027667 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for HCG22 (see all 12):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2670269CNV Deletion23128226
    esv2731809CNV Deletion23290073
    esv2731805CNV Deletion23290073
    esv2731808CNV Deletion23290073
    esv2731791CNV Deletion23290073
    esv4161CNV Deletion18987735
    esv27565CNV Loss19812545
    nsv884133CNV Loss21882294
    dgv6536n71CNV Loss21882294
    nsv884132CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing HCG22
    DNA2.0 Custom Variant and Variant Library Synthesis for HCG22

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 613918    OMIM disorders: --

    1 disease for HCG22:    
    About MalaCards
    follicular lymphoma


    Find genes that share disorders with HCG22           About GenesLikeMe

    Genetic Association Database (GAD): HCG22
    Human Genome Epidemiology (HuGE) Navigator: HCG22 (2 documents)

    Export disorders for HCG22 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 HCG22 gene, integrated from 10 sources (see all 14):
    (articles sorted by number of sources associating them with HCG22)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning of two novel mucin-like genes in the disease- susceptibility locus for diffuse panbronchiolitis. (PubMed id 20981447)1, 2 Hijikata M.... Keicho N. (Hum. Genet. 2011)
    2. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. (PubMed id 21051598)1, 4  ....Zhao M. (Science 2010)
    3. 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)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 3 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children. (PubMed id 23263863)1 Li J....Sleiman P.M. (Hum. Mol. Genet. 2013)
    6. Novel associations for hypothyroidism include known autoimmune risk loci. (PubMed id 22493691)1 Eriksson N....Do C.B. (PLoS ONE 2012)
    7. Identification of a susceptibility locus in STAT4 for BehAset's disease in Han Chinese in a genome-wide association study. (PubMed id 23001997)1 Hou S....Yang P. (Arthritis Rheum. 2012)
    8. Multiple loci are associated with white blood cell phenotypes. (PubMed id 21738480)1 Nalls M.A....Ganesh S.K. (PLoS Genet. 2011)
    9. A genome-wide association study identifies two new risk loci for Graves' disease. (PubMed id 21841780)4 Chu X....Song H.D. (Nat. Genet. 2011)
    10. Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regions associated with BehAset's disease. (PubMed id 20622878)4 Remmers E.F....GA1l A. (Nat. Genet. 2010)

    (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: 285834 HGNC: 27780 AceView: HCG22 Ensembl:ENSG00000228789 euGenes: HUgn285834
    ECgene: HCG22 H-InvDB: HCG22

    (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 HCG22 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 HCG22 gene:
    Search GeneIP for patents involving HCG22

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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     Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

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     inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HCG22
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     Search LSBio for Antibodies for HCG22
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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 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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