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

HDGFRP2 Gene

protein-coding   GIFtS: 41
GCID: GC19P004472

HDGFRP2


  Search for HDGFRP2
in our new
 Human Malady Compendium 
Biological research products
for HDGFRP2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Hepatoma-Derived Growth Factor 22 3
HDGF-22 3
HDGF22 3
HRP-22 3
Hepatoma-Derived Growth Factor-Related Protein 22

External Ids:    Entrez Gene: 847172   Ensembl: ENSG000001676747   UniProtKB: Q7Z4V53   

Export aliases for HDGFRP2 gene to outside databases

Previous GC identifer: GC19P004234


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

Entrez Gene summary for HDGFRP2:
This gene encodes a member of the hepatoma-derived growth factor (HDGF) family. Two alternatively spliced transcript
variants encoding slightly different isoforms have been found for this gene. (provided by RefSeq, Jul 2008)




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.1  NT_011255.14  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for HDGFRP2
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHDGFRP2 promoter sequence
   Search SABiosciences Chromatin IP Primers for HDGFRP2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HDGFRP2


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

Entrez Gene cytogenetic band: 19p13.3   Ensembl cytogenetic band:  19p13.3   

HDGFRP2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HDGFRP2 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P004472:  view genomic region     (about GC identifiers)

Start:
4,472,255 bp from pter      End:
4,502,223 bp from pter
Size:
29,969 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: HDGR2_HUMAN, Q7Z4V5 (See protein sequence)
Recommended Name: Hepatoma-derived growth factor-related protein 2  
Size: 671 amino acids; 74317 Da
Subunit: May interact with trimethylated histone H3 (H3K79me3)
3 PDB 3D structures from and Proteopedia for HDGFRP2:
3EAE (3D)        3QBY (3D)        3QJ6 (3D)    
Secondary accessions: Q96GI5 Q9BW08
Alternative splicing: 2 isoforms:  Q7Z4V5-1   Q7Z4V5-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for HDGFRP2: NX_Q7Z4V5

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q7Z4V5

  • HDGFRP2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001001520.1  NP_116020.1  

    ENSEMBL proteins: 
     ENSP00000301284   ENSP00000468044   ENSP00000465267   ENSP00000467617   ENSP00000467966  
     ENSP00000468175   ENSP00000467513   ENSP00000468340   ENSP00000465276   ENSP00000464738  

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    Browse Proteins at Uscn

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--


    HDGFRP2 for ontologies           About GeneDecksing



    HDGFRP2 Antibody Products: 
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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    HDGFRP2 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR017923 TFIIS_N
     IPR000313 PWWP
     IPR021567 LEDGF

    Graphical View of Domain Structure for InterPro Entry Q7Z4V5

    ProtoNet protein and cluster: Q7Z4V5

    1 Blocks protein family: IPB000313 PWWP domain

    UniProtKB/Swiss-Prot: HDGR2_HUMAN, Q7Z4V5
    Similarity: Belongs to the HDGF family
    Similarity: Contains 1 PWWP domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate HDGFRP2:
    hsa-miR-548d-3p
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    Inhib. RNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--


    HDGFRP2 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Hdgfrp2tm1Lex for HDGFRP2
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Hdgfrp2):
     cellular  homeostasis/metabolism 

    HDGFRP2 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HDGFRP2

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

    5/9 Interacting proteins for HDGFRP2 (Q7Z4V51, 3 ENSP000003012844) via UniProtKB, MINT, STRING, and/or I2D (see all 9)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARRB1P494071, 3, ENSP000003771414EBI-1049136,EBI-743313 I2D: score=2 STRING: ENSP00000377141
    SIAH1Q8IUQ43I2D: score=5 
    RAD54LQ926983I2D: score=4 
    PIH1D1Q9NWS03I2D: score=3 
    ARRB2P321213I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--


    HDGFRP2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 HDGFRP2
    Search CenterWatch for drugs/clinical trials and news about HDGFRP2 / HDGR2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HDGFRP2 gene (2 alternative transcripts): 
    NM_001001520.1  NM_032631.2  

    Unigene Cluster for HDGFRP2:

    Hepatoma-derived growth factor-related protein 2
    Hs.43071  [show with all ESTs]
    Unigene Representative Sequence: AB208892
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000301284(uc002map.3 uc002mao.3 uc010dtz.1 uc002maq.1 uc010dua.3)
    ENST00000586684 ENST00000589486 ENST00000592691 ENST00000590872 ENST00000587016
    ENST00000592417 ENST00000586428 ENST00000591328 ENST00000588271

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate HDGFRP2:
    hsa-miR-548d-3p
    SwitchGear 3'UTR luciferase reporter plasmidHDGFRP2 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AB208892.1 AF294267.1 AK027353.1 AY358600.1 BC000755.2 BC009449.1 BC126984.1 BC126985.1 

    10 DOTS entries:

    DT.211031  DT.95297177  DT.75103068  DT.99961788  DT.100754253  DT.121499827  DT.100026594  DT.100726578 
    DT.100777763  DT.97825722 

    24/177 AceView cDNA sequences (see all 177):

    CR611041 BM681995 BX438858 CR590767 BE907713 AY358600 BM729060 AL539869 
    BM789312 NM_032631 BU165411 BQ064366 BQ962664 BQ898864 AI565918 BC000755 
    BQ685764 AL520441 BF984461 BX090267 AI479411 BM713639 AK027353 BX462129 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for HDGFRP2 (see all 6)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b · 16c · 16d
    SP1:                                                                                                                                    
    SP2:                                                                                            -     -     -                           
    SP3:        -                                                                                                                           
    SP4:                                                                                                                                    
    SP5:                                                                                                              -                     



    (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

    HDGFRP2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AAATGACTAT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See HDGFRP2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HDGFRP2

    SOURCE GeneReport for Unigene cluster: Hs.43071
        SABiosciences Custom PCR Arrays for HDGFRP2
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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for HDGFRP2 gene from 7/19 species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hdgfrp21 , 5 hepatoma-derived growth factor, related protein 21, 5 80.27(n)1
    83.76(a)1
      17 (29.15 cM)5
    151931  NM_008233.21  NP_032259.11 
     560796575 
    chicken
    (Gallus gallus)
    Aves LOC7723021 hepatoma-derived growth factor-related protein 2-like 70.23(n)
    71.38(a)
      772302  XM_001235457.2  XP_001235458.2 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    --
    51(a)
    29(a)
    1 ↔ 1
    possible ortholog
    GL343757.1(128214-151079)
    2(105347723-105348226)
    African clawed frog
    (Xenopus laevis)
    Amphibia 480209182   -- 75.98(n)    48020918 
    zebrafish
    (Danio rerio)
    Actinopterygii BC055551.12   -- 78.58(n)    BC055551.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG79466
    --
    17(a)
    1 → many
    3R(25878236-25880419)
    worm
    (Caenorhabditis elegans)
    Secernentea C06A5.36
    --
    10(a)
    possible ortholog
    I(5986494-5990583)


    ENSEMBL Gene Tree for HDGFRP2 (if available)
    TreeFam Gene Tree for HDGFRP2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HDGFRP2 gene
    HDGF2  PSIP12  HDGFL12  HDGFRP32  
    18/29 SIMAP similar genes for HDGFRP2 using alignment to 12 protein entries:     HDGR2_HUMAN (see all proteins) (see all similar genes):
    ARL6IP5    CALCOCO2    KIAA0101    SMYD4    C1orf143    COQ5
    COPS7B    EEF1E1    PARK2    RAD51    SEC14L3    ZNF564
    TBC1D22A    FAM175A    FP1523    PTPLA    PSIP1    HDGFRP3

    HDGFRP2 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/26 NCBI SNPs in HDGFRP2 are shown (see all 26    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1173155141,2
    C,F,--4263239(+) ACTTAC/TCNNNN 2 -- int11Minor allele frequency- T:0.03NA 120
    rs766404121,2
    --4263285(+) GGGGAC/TCCTGG 2 -- int10--------
    rs775731151,2
    C,F,--4263615(+) TTCCCC/TGGCTC 2 -- ut311Minor allele frequency- T:0.04EA 120
    rs104213021,2
    C,F,H,--4263640(+) CAGAGA/GACTGT 2 -- ut31 ese311Minor allele frequency- G:0.10NS EA NA CSA WA 1199
    rs45070261,2
    H--4264125(+) GCTGGG/CAGGGT 2 -- ds50014Minor allele frequency- C:0.00NS EA 418
    rs763690501,2
    C,F,--4264156(+) GAGCCG/ACTGCT 2 -- ds50011Minor allele frequency- A:0.02WA 118
    rs603073711,2
    C,--4264166(+) TAGCCG/AACAGT 2 -- ds50012Minor allele frequency- A:0.05WA 120
    rs1873927921,2
    --4501696(+) GTCACA/TCACTT 1 -- ds50010--------
    rs357994541,2
    C,F,--4501801(+) AGGGCG/AGCACT 1 -- ds50012Minor allele frequency- A:0.50NA 4
    rs1409003281,2
    --4501902(+) CACACC/TGCCTT 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for HDGFRP2 (4472255 - 4502223 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for HDGFRP2: --
    Human Gene Mutation Database (HGMD): HDGFRP2

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HDGFRP2
    DNA2.0 Custom Variant and Variant Library Synthesis for HDGFRP2

    (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.)
    About This Section

    HDGFRP2 for disorders           About MalaCards

    HDGFRP2 for disorders           About GeneDecksing


    Export disorders for HDGFRP2 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 HDGFRP2 gene, integrated from 9 sources (see all 17):
    (articles sorted by number of sources associating them with HDGFRP2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
    2. Biochemical and genetic analyses of integrase-interacting proteins lens epithelium-derived growth factor (LEDGF)/p75 and hepatoma-derived growth factor related protein 2 (HRP2) in preintegration complex function and HIV-1 replication. (PubMed id 16337983)1, 9 Vandegraaff N....Engelman A. (2006)
    3. A high-throughput approach for measuring temporal chan ges in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (2012)
    4. Structural and histone binding ability characterizations of human PWWP domains. (PubMed id 21720545)1 Wu H.... Min J. (2011)
    5. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    6. Genome-wide YFP fluorescence complementation screen id entifies new regulators for telomere signaling in human cells. (PubMed id 21044950)1 Lee O.H....Songyang Z. (2011)
    7. Functional specialization of beta-arrestin interactions revealed by proteomic analysis. (PubMed id 17620599)1 Xiao K....Lefkowitz R.J. (2007)
    8. Large-scale mapping of human protein-protein interactions by mass spectrometry. (PubMed id 17353931)1 Ewing R.M.... Figeys D. (2007)
    9. Identification of the LEDGF/p75 HIV-1 integrase-interaction domain and NLS reveals NLS-independent chromatin tethering. (PubMed id 15797927)1 Vanegas M....Poeschla E.M. (2005)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)

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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: 84717 AceView: HDGF2 Ensembl:ENSG00000167674 euGenes: HUgn84717

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    (Patent information from GeneIP,
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    Patent Information for HDGFRP2 gene:
    Search GeneIP for patents involving HDGFRP2

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