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HHLA1 Gene

protein-coding   GIFtS: 43
GCID: GC08M133074

HERV-H LTR-Associating 1


(Previous symbol: PLA2L)
  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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Aliases
HERV-H LTR-Associating 11 2
PLA2L1 2
HERV-H LTR-Associating Protein 12

External Ids:    HGNC: 49041   Entrez Gene: 100862   Ensembl: ENSG000001322977   OMIM: 6041095   UniProtKB: C9JL843   

Export aliases for HHLA1 gene to outside databases

Previous GC identifers: GC08M131787 GC08M133108 GC08M132746 GC08M133032 GC08M133145 GC08M128391


(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 HHLA1 Gene:
HHLA1 (HERV-H LTR-associating 1) is a protein-coding gene. Diseases associated with HHLA1 include benign paroxysmal positional nystagmus, and oligohydramnios.


(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:
NC_000008.11  NC_018919.2  NT_008046.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the HHLA1 gene promoter:
         Lmo2   Nkx2-5   HNF-3beta   Evi-1   POU2F1   POU2F1a   FOXO4   POU2F1b   POU2F1c   RSRFC4   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for HHLA1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HHLA1


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

Entrez Gene cytogenetic band: 8q24   Ensembl cytogenetic band:  8q24.22   HGNC cytogenetic band: 8q24

HHLA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HHLA1 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M133074:  view genomic region     (about GC identifiers)

Start:
133,073,733 bp from pter      End:
133,123,406 bp from pter
Size:
49,674 bases      Orientation:
minus strand

(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: HHLA1_HUMAN, C9JL84 (See protein sequence)
Recommended Name: HERV-H LTR-associating protein 1 precursor  
Size: 531 amino acids; 58297 Da
Alternative splicing: 2 isoforms:  C9JL84-1   C9JL84-2   (Expressed in teratocarcinoma cell lines)

Explore the universe of human proteins at neXtProt for HHLA1: NX_C9JL84

Explore proteomics data for HHLA1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn79, Asn143, Asn161
  • Modification sites at PhosphoSitePlus

  • See HHLA1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001138567.1  
    ENSEMBL proteins: 
     ENSP00000407107   ENSP00000388322  

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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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    ProtoNet protein and cluster: C9JL84


    (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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    Molecular Function:
         Genatlas biochemistry entry for HHLA1:
    HERVH LTR-associating 1,linked to OC90 by intergenic splicing

    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
    HHLA1_HUMAN, C9JL84: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    lysosome1
    mitochondrion1
    plasma membrane1

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

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

    HHLA1 for ontologies           About GeneDecksing


    (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 HHLA1
    Interactions:

        Search GeneGlobe Interaction Network for HHLA1

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for HHLA1 (ENSP000003883224) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    BMPR2ENSP000003637084STRING: ENSP00000363708
    About this table

    (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 HHLA1



    (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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    REFSEQ mRNAs for HHLA1 gene (2 alternative transcripts): 
    NM_005712.1  NM_001145095.1  

    Unigene Cluster for HHLA1:

    HERV-H LTR-associating 1
    Hs.285026  [show with all ESTs]
    Unigene Representative Sequence: NM_001145095
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000473291 ENST00000434736 ENST00000414222(uc003yth.2 uc011liy.1)

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate HHLA1 (see all 9):
    hsa-miR-4303 hsa-miR-3164 hsa-miR-205 hsa-miR-224 hsa-miR-526b hsa-miR-513a-5p hsa-miR-3921 hsa-miR-889
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      QuantiFast Probe-based Assays in human, mouse, rat HHLA1

    Additional mRNA sequence: AK022619.1 

    2 DOTS entries:

    DT.92048812  DT.120635422 

    2 AceView cDNA sequences:

    AF110315 NM_005712 

    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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    HHLA1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACTATAATCT
    HHLA1 Expression
    About this image


    HHLA1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
             Human embryonic stem cells (family)
    HHLA1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HHLA1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.285026
        Custom PCR Arrays for HHLA1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HHLA1

    (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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    This gene was present in the common ancestor of chordates.

    Orthologs for HHLA1 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hhla11 , 5 HERV-H LTR-associating 11, 5 72.78(n)1
    61.62(a)1
      15 (29.16 cM)5
    6544981  NM_001145096.11  NP_001138568.11 
     659224435 
    chicken
    (Gallus gallus)
    Aves HHLA11 HERV-H LTR-associating 1 66.48(n)
    62.39(a)
      101749300  XM_004940093.1  XP_004940150.1 
    lizard
    (Anolis carolinensis)
    Reptilia HHLA16
    HERV-H LTR-associating 1
    40(a)
    1 ↔ 1
    4(268852-299768)
    zebrafish
    (Danio rerio)
    Actinopterygii HHLA16
    HERV-H LTR-associating 1
    64(a)
    1 ↔ 1
    2(43081596-43082550) ENSDARG00000087842


    ENSEMBL Gene Tree for HHLA1 (if available)
    TreeFam Gene Tree for HHLA1 (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 HHLA1 (see all 1146)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1921599841,2
    --133073758(+) ATGACA/GTTACG 1 -- ut310--------
    rs1826689751,2
    --133073772(+) GTAACC/TGCACA 1 -- ut310--------
    rs1413021531,2
    --133073775(+) ACTGCA/GCAATC 1 -- ut310--------
    rs1450350921,2
    C--133073836(+) GCTAAC/TCACTG 1 -- ut310--------
    rs1877936341,2
    --133073923(+) CTATCC/GCCTAA 1 -- ut310--------
    rs1126876601,2
    C,F--133073954(+) GAAGGG/AGTCAA 1 -- ut311Minor allele frequency- A:0.50CSA 2
    rs1504008121,2
    C--133073986(+) ACCAGC/TTGGAC 1 -- ut310--------
    rs1927810701,2
    --133074049(+) CTGTTA/GTGGCT 1 -- ut310--------
    rs1381143491,2
    C--133074098(+) CTGAGA/CCTTTG 1 -- ut310--------
    rs1841522391,2
    --133074099(+) TGAGCC/TTTTGT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for HHLA1 (133073733 - 133123406 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for HHLA1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv507494CNV Insertion20534489
    nsv6401CNV Insertion18451855
    nsv891453CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
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    (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: 604109    OMIM disorders: --

    2 diseases for HHLA1:    
    About MalaCards
    benign paroxysmal positional nystagmus    oligohydramnios

    2 diseases from the University of Copenhagen DISEASES database for HHLA1:
    Benign paroxysmal positional nystagmus     Oligohydramnios

    HHLA1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): HHLA1

    Export disorders for HHLA1 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 HHLA1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with HHLA1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Intergenic splicing between a HERV-H endogenous retrovirus and two adjacent human genes. (PubMed id 10329003)1, 2, 3, 9 Kowalski P.E.... Mager D.L. (Genomics 1999)
    2. Web-based, participant-driven studies yield novel genetic associations for common traits. (PubMed id 20585627)1, 4 Eriksson N....Mountain J. (PLoS Genet. 2010)
    3. Splicing of a human endogenous retrovirus to a novel phospholipase A2 related gene. (PubMed id 8382789)1, 2 Feuchter-Murthy A.E.... Mager D.L. (Nucleic Acids Res. 1993)
    4. DNA sequence and analysis of human chromosome 8. (PubMed id 16421571)2 Nusbaum C....Lander E.S. (Nature 2006)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. A human endogenous retrovirus suppresses translation of an associated fusion transcript, PLA2L. (PubMed id 9621083)9 Kowalski P.E. and Mager D.L. (J. Virol. 1998)

    (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: 10086 HGNC: 4904 AceView: HHLA1 Ensembl:ENSG00000132297 euGenes: HUgn10086
    ECgene: HHLA1 H-InvDB: HHLA1

    (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 HHLA1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for HHLA1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HHLA1 gene:
    Search GeneIP for patents involving HHLA1

    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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