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HIRIP3 Gene

protein-coding   GIFtS: 55
GCID: GC16M030005

HIRA Interacting Protein 3

(Previous name: HIRA-interacting protein 3)
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(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
HIRA Interacting Protein 31 2
HIRA-Interacting Protein 31 2

External Ids:    HGNC: 49171   Entrez Gene: 84792   Ensembl: ENSG000001499297   OMIM: 6033655   UniProtKB: Q9BW713   

Export aliases for HIRIP3 gene to outside databases

Previous GC identifers: GC16P029153 GC16M030326 GC16M030002 GC16M030041 GC16M029911 GC16M027665


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for HIRIP3 Gene:
The HIRA protein shares sequence similarity with Hir1p and Hir2p, the two corepressors of histone gene
transcription characterized in the yeast, Saccharomyces cerevisiae. The structural features of the HIRA protein
suggest that it may function as part of a multiprotein complex. Several cDNAs encoding HIRA-interacting proteins,
or HIRIPs, have been identified. In vitro, the protein encoded by this gene binds HIRA, as well as H2B and H3
core histones, indicating that a complex containing HIRA-HIRIP3 could function in some aspects of chromatin and
histone metabolism. Alternatively spliced transcript variants encoding distinct isoforms have been found for this
gene.(provided by RefSeq, Aug 2011)

GeneCards Summary for HIRIP3 Gene:
HIRIP3 (HIRA interacting protein 3) is a protein-coding gene.

UniProtKB/Swiss-Prot: HIRP3_HUMAN, Q9BW71
Function: May play a role in chromatin function and histone metabolism via its interaction with HIRA and histones

Gene Wiki entry for HIRIP3 Gene


(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_000016.9  NC_018927.2  NT_187260.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the HIRIP3 gene promoter:
         E2F-4   E2F-3a   E2F-5   Nkx2-5   E2F-2   AREB6   RORalpha1   E2F   E2F-1   ARP-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHIRIP3 promoter sequence
   Search Chromatin IP Primers for HIRIP3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HIRIP3


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

Entrez Gene cytogenetic band: 16p11.2   Ensembl cytogenetic band:  16p11.2   HGNC cytogenetic band: 16p12.1

HIRIP3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HIRIP3 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M030005:  view genomic region     (about GC identifiers)

Start:
30,003,645 bp from pter      End:
30,007,757 bp from pter
Size:
4,113 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: HIRP3_HUMAN, Q9BW71 (See protein sequence)
Recommended Name: HIRA-interacting protein 3  
Size: 556 amino acids; 61957 Da
Subunit: Interacts with HIRA. Weak interaction with histones H2B and H3. Interacts with CK2
Secondary accessions: H3BSR3 O75707 O75708
Alternative splicing: 3 isoforms:  Q9BW71-1   Q9BW71-2   Q9BW71-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for HIRIP3: NX_Q9BW71

Explore proteomics data for HIRIP3 at MOPED

Post-translational modifications: 

  • Phosphorylated by CK21
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See HIRIP3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001184252.1  NP_003600.2  

    ENSEMBL proteins: 
     ENSP00000279392   ENSP00000456824  

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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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    1 InterPro protein domain:
     IPR019098 Histone_chaperone_domain_CHZ

    Graphical View of Domain Structure for InterPro Entry Q9BW71

    ProtoNet protein and cluster: Q9BW71


    Find genes that share domains with HIRIP3           About GenesLikeMe


    (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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HIRP3_HUMAN, Q9BW71
    Function: May play a role in chromatin function and histone metabolism via its interaction with HIRA and histones

         Genatlas biochemistry entry for HIRIP3:
    HIRA-interacting protein 3,widely expressed an histone (H2B,H3) binding protein,directly interacting with the
    WD-repeat protein HIRA

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI9710638
         
    Find genes that share ontologies with HIRIP3           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for HIRIP3:
     Increased gamma-H2AX phosphory 

         1 MGI phenotypic allele for Hirip3 (no phenotypes)

    Find genes that share phenotypes with HIRIP3           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HIRIP3
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    miRNA
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    miRTarBase miRNAs that target HIRIP3:
    hsa-mir-877-3p (MIRT037067)

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    3 qRT-PCR Assays for microRNAs that regulate HIRIP3:
    hsa-miR-627 hsa-miR-924 hsa-miR-599
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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
    HIRP3_HUMAN, Q9BW71: Nucleus. Note=Nuclear throughout the cell cycle and is excluded from condensed chromatin
    during mitosis
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    golgi apparatus1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA17391060

    Find genes that share ontologies with HIRIP3           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 HIRIP3
    Interactions:

        GeneGlobe Interaction Network for HIRIP3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    Selected Interacting proteins for HIRIP3 (Q9BW712, 3 ENSP000002793924) via UniProtKB, MINT, STRING, and/or I2D (see all 27)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053, ENSP000003529804I2D: score=1 STRING: ENSP00000352980
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006333chromatin assembly or disassembly TAS9710638

    Find genes that share ontologies with HIRIP3           About GenesLikeMe



    (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 HIRIP3 (HIRP3)

    1 HMDB Compound for HIRIP3    About this table
    CompoundSynonyms CAS #PubMed Ids
    Docosanoyl-CoAbehenoyl-CoA (see all 2)----



    (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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    REFSEQ mRNAs for HIRIP3 gene (2 alternative transcripts): 
    NM_001197323.1  NM_003609.4  

    Unigene Cluster for HIRIP3:

    HIRA interacting protein 3
    Hs.567370  [show with all ESTs]
    Unigene Representative Sequence: NM_003609
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000279392(uc002dve.3 uc002dvf.3) ENST00000564026 ENST00000563053
    ENST00000563680 ENST00000566471 ENST00000565996 ENST00000568880
    miRNA
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    3 qRT-PCR Assays for microRNAs that regulate HIRIP3:
    hsa-miR-627 hsa-miR-924 hsa-miR-599
    SwitchGear 3'UTR luciferase reporter plasmidHIRIP3 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat HIRIP3
      QuantiFast Probe-based Assays in human, mouse, rat HIRIP3

    Additional mRNA sequence: 

    AJ223349.1 AJ223350.1 AJ223351.2 AK312504.1 BC000588.2 

    17 DOTS entries:

    DT.92439846  DT.95268337  DT.92026640  DT.310247  DT.102844277  DT.92445465  DT.91798357  DT.100770026 
    DT.100888195  DT.120696685  DT.95268349  DT.100691939  DT.92439863  DT.100888204  DT.91988194  DT.92439845 
    DT.95229021 

    Selected AceView cDNA sequences (see all 189):

    BM671426 BX101682 BU729840 BM904336 BM672428 BE207110 BQ945868 BQ896302 
    BU730222 BQ682147 BF229550 AA394077 BU902630 BM702893 CB152379 BM904300 
    Z40329 AL710271 BE326341 BQ953306 NM_003609 CR604428 CR624147 BM550751 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for HIRIP3 (see all 10)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3a · 3b · 3c · 3d ^ 4a · 4b · 4c · 4d · 4e ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c
    SP1:                                            -     -           -                             -     -                                       
    SP2:                                            -     -           -     -     -     -     -     -     -                                       
    SP3:                                            -     -           -                                                                           
    SP4:                                                              -     -     -     -     -     -     -                                       
    SP5:                                                                                                                                          


    ECgene alternative splicing isoforms for HIRIP3

    (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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    HIRIP3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TACAAAGCAT
    HIRIP3 Expression
    About this image

    HIRIP3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HIRIP3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.567370

    UniProtKB/Swiss-Prot: HIRP3_HUMAN, Q9BW71
    Tissue specificity: Widely expressed. Isoform 1 is predominant in skeletal muscle. Isoform 2 is predominant in
    liver and heart

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    In Situ
    Assay Products:
     

     
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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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    This gene was present in the common ancestor of chordates.

    Orthologs for HIRIP3 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hirip31 , 5 HIRA interacting protein 31, 5 70.86(n)1
    61.71(a)1
      7 (69.25 cM)5
    2338761  NM_172746.31  NP_766334.11 
     1268619725 
    lizard
    (Anolis carolinensis)
    Reptilia HIRIP36
    HIRA interacting protein 3
    28(a)
    1 ↔ 1
    GL343606.1(329912-342935)
    zebrafish
    (Danio rerio)
    Actinopterygii hirip36
    HIRA interacting protein 3
    29(a)
    1 ↔ 1
    3(14798115-14815085) ENSDARG00000027749


    ENSEMBL Gene Tree for HIRIP3 (if available)
    TreeFam Gene Tree for HIRIP3 (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 HIRIP3 (see all 72)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1173483771,2
    F--30004115(+) GGGGTA/GGGCGG 2 -- ut311Minor allele frequency- G:0.01EA 120
    rs1914489181,2
    --30004124(+) GGGCAA/GCACAG 2 -- ut310--------
    rs1827186711,2
    --30004160(+) GTCTGA/GTGGCT 2 -- ut310--------
    rs1875258061,2
    --30004209(+) GAACCC/TGGGGG 2 -- ut310--------
    rs3775283891,2
    C--30004360(+) ATAAAC/TCCTTA 2 -- ut310--------
    rs1997916731,2
    C--30004498(+) CATGTA/GTCAAG 2 -- ut310--------
    rs2014276471,2
    --30004516(+) CCTGGC/GGGTGG 2 -- ut310--------
    rs1435206001,2
    C--30004593(+) GGGACG/AGGGCC 3 /R /C mis1 ut311Minor allele frequency- A:0.00NA 4544
    rs1462783671,2
    C,F--30004603(+) CGCTCC/G/TTCATC 5 E D mis1 syn1 ut312NA EU 5865
    rs1393840131,2
    C--30004623(+) GGTCCG/ATCGGT 3 /R /W mis1 ut311Minor allele frequency- A:0.00NA 4542

    HapMap Linkage Disequilibrium report for HIRIP3 (30003645 - 30007757 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for HIRIP3:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv997840CNV Deletion20482838
    dgv2668n71CNV Loss21882294
    nsv905717CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HIRIP3
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    (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: 603365    OMIM disorders: --

    2 diseases from the University of Copenhagen DISEASES database for HIRIP3:
    DiGeorge syndrome     Velocardiofacial syndrome

    Find genes that share disorders with HIRIP3           About GenesLikeMe

    Genetic Association Database (GAD): HIRIP3
    Human Genome Epidemiology (HuGE) Navigator: HIRIP3 (1 document)

    Export disorders for HIRIP3 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 HIRIP3 gene, integrated from 10 sources (see all 30):
    (articles sorted by number of sources associating them with HIRIP3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Core histones and HIRIP3, a novel histone-binding protein, directly interact with WD repeat protein HIRA. (PubMed id 9710638)1, 2, 3, 9 Lorain S.... Lipinski M. (Mol. Cell. Biol. 1998)
    2. HIRIP3 is a nuclear phosphoprotein interacting with and phosphorylated by the serine-threonine kinase CK2. (PubMed id 17391060)1, 2, 9 Assrir N.... Lipinski M. (Biol. Chem. 2007)
    3. Association and mutation analyses of 16p11.2 autism candidate genes. (PubMed id 19242545)1, 4 Kumar R.A....Christian S.L. (PLoS ONE 2009)
    4. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (Nat. Biotechnol. 2006)
    5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    7. Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. (PubMed id 23455922)1 Varjosalo M....Superti-Furga G. (Nat. Methods 2013)
    8. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    9. The protein interaction landscape of the human CMGC kinase group. (PubMed id 23602568)1 Varjosalo M....Gstaiger M. (Cell Rep 2013)
    10. A high-throughput approach for measuring temporal changes in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (Nat. Methods 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 8479 HGNC: 4917 AceView: HIRIP3 Ensembl:ENSG00000149929 euGenes: HUgn8479
    ECgene: HIRIP3 H-InvDB: HIRIP3

    (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 HIRIP3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HIRIP3 gene:
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