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ID3 Gene

protein-coding   GIFtS: 65

GC01M023756
inhibitor of DNA binding 3, dominant negative helix-loop-helix protein
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
1R21 3
HEIR-1 1, 2, 3
OTTHUMP00000003263 2
bHLHb25 1, 2
Descriptions
Helix-loop-helix protein HEIR-1 3
ID-like protein inhibitor HLH 1R21 3
Inhibitor of DNA binding 3 2, 3
inhibitor of DNA binding 3, dominant negative
helix-loop-helix protein 2
External Ids
HGNC: 53621
Entrez Gene: 33992
UniProtKB: Q025353
Ensembl: ENSG000001173187
Search outside databases for aliases for ID3 gene

Previous GC identifers: GC01M023442 GC01M022955 GC01M023353 GC01M023629

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for ID3:
Members of the ID family of helix-loop-helix (HLH) proteins lack a basic DNA-binding domain and
inhibit transcription through formation of nonfunctional dimers that are incapable of binding to
DNA.[supplied by OMIM]

UniProtKB/Swiss-Prot: ID3_HUMAN, Q02535
Function: ID (inhibitor of DNA binding) HLH proteins lack a basic DNA-binding domain but are able
to form heterodimers with other HLH proteins, thereby inhibiting DNA binding. ID-3 inhibits the
binding of E2A-containing protein complexes to muscle creatine kinase E-box enhancer. May inhibit
other transcription factors

Gene Wiki entry for ID3

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the ID3 gene  

Entrez Gene cytogenetic band: 1p36.13-p36.12   Ensembl cytogenetic band:  1p36.12   HGNC cytogenetic band: 1p36.13-p36.12

ID3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M023756:     (about GC identifiers)

Start:
23,756,996 bp from pter
End:
23,758,909 bp from pter
Size:
1,914 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000001.9  NT_004610.18  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: ID3_HUMAN, Q02535 (See protein sequence)
Recommended Name: DNA-binding protein inhibitor ID-3  
Size: 119 amino acids; 12969 Da
Subunit: Interacts with COPS5 and COPS7A (By similarity). Homodimer, and heterodimer with other HLH
proteins
Subcellular location: Nucleus
Secondary accessions: O75641

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_002158.3  

    ENSEMBL proteins: 
    ENSP00000363689 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (ID3)
    Human Recombinant Proteins from Abnova (ID3)
                  OriGene Purified Recombinant Human Protein: ID3 

    1 Gene Ontology (GO) cellular component term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634 nucleus IEA--
    About this table

    Antibodies for ID3: 
    Browse Antibodies Central at Invitrogen
    Millipore Mono- and Polyclonal Antibodies for the study of ID3
    Sigma-Aldrich Antibodies for ID3
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (ID3), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (ID3)
    Novus Biologicals Antibodies for ID3

    Assays for ID3: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

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

    1 InterPro domain/family:
     IPR001092 HLH_basic


       GeneDecks  ID3 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q02535

    ProtoNet protein and cluster: Q02535

    1 Blocks protein family: IPB001092 Basic helix-loop-helix dimerization domain bHLH

    UniProtKB/Swiss-Prot: ID3_HUMAN, Q02535
    Similarity: Contains 1 basic helix-loop-helix (bHLH) domain

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (ID3)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (ID3)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_002167

                  Applied Biosystems Silencer® siRNAs for ID3

                  Sigma-Aldrich siRNA for ID3  
                         Sigma-Aldrich shRNA for ID3  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for ID3
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_002167
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_002167
                                     untagged cDNA clone in CMV expression vector: NM_002167 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_002167

    UniProtKB/Swiss-Prot: ID3_HUMAN, Q02535
    Function: ID (inhibitor of DNA binding) HLH proteins lack a basic DNA-binding domain but are able
    to form heterodimers with other HLH proteins, thereby inhibiting DNA binding. ID-3 inhibits the
    binding of E2A-containing protein complexes to muscle creatine kinase E-box enhancer. May inhibit
    other transcription factors
    Induction: By phorbol 12-myristate 13-acetate (PMA)

    Genatlas biochemistry entry for ID3:
    inhibitor of DNA binding 3,mouse ld-3 related,expressed during early development and in adult
    tissues,inhibing transcription factors of the basic helix loop helix family, required for
    neurogenesis and angiogenesis

    8 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Id3):

    embryogenesisgrowth/sizehematopoietic systemimmune system
    lethality-prenatal/perinatalnervous systemtumorigenesis

    3 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003714 transcription corepressor activity TAS8437843
    GO:0008134 transcription factor binding IEA--
    GO:0019904 protein domain specific binding IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


    1 Kegg Pathway  (Kegg details for ID3):
     hsa04350 TGF-beta signaling pathway

       GeneDecks  ID3 for the pathways selected above  
    About GeneDecksing
     Gene Network CentralTM Interacting Genes and Proteins Network for  ID3 


    5/16 Interacting proteins for ID3 (ENSP000003636893) via UniProtKB, MINT, and/or STRING (see all 16 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TCF3ENSP000002629653STRING (score=.989)
    TCF4ENSP000003464403STRING (score=.933)
    ID4ENSP000003679723STRING (score=.931)
    BMP4ENSP000002454513STRING (score=.926)
    MYOD1ENSP000002500033STRING (score=.894)
    About this table

    5/10 Gene Ontology (GO) biological process terms (links to tree view) (see all 10 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0006275 regulation of DNA replication IEA--
    GO:0007275 multicellular organismal development TAS1628620
    GO:0007507 heart development IEA--
    GO:0009611 response to wounding IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for ID3
    2 Novoseek chemical compound relationships for ID3 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    oxygen 0.00 2 19054058 (2)
    zinc 0.00 1 10575541 (1)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (ID3)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (ID3)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_002167

                  Sigma-Aldrich siRNA for ID3  
                         Sigma-Aldrich shRNA for ID3  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_002167  

    REFSEQ mRNAs for ID3 gene: 

    NM_002167.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_002167  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_002167
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_002167
                                     untagged cDNA clone in CMV expression vector: NM_002167 

    Additional cDNA sequence: 

    AK225965.1 AK290003.1 BC003107.1 BT006791.1 CR597388.1 CR603067.1 CR611504.1 CR612668.1 
    CR614670.1 CR615457.1 CR620515.1 CR623483.1 D28449.1 X66924.1 X69111.1 

    10 DOTS entries:

    DT.448517  DT.92452265  DT.100817038  DT.100817039  DT.97855621  DT.95365730  DT.95365717  DT.121403793 
    DT.92452272  DT.95099597 

    24/562 AceView cDNA sequences (see all 562 ):

    H89353 CA420836 CR623483 AA516007 BF061101 BQ008635 BQ014563 AA583583 
    AI949079 AA425764 AI077534 CR612668 BU733493 CR611504 AA987439 CD671237 
    CR614670 N50460 BQ005231 BM739564 BE221233 BF439510 CD671238 CR597388 

    highest scoring ESTs for ID3:

    AA310279 AA525306 AA576713 AI992066 AL048518 AL697702 AL708993 AW163787 AW166245 AW328591 

    Unigene Cluster for ID3:

    Inhibitor of DNA binding 3, dominant negative helix-loop-helix protein
    Hs.76884  [show with all ESTs]
    Unigene Representative Sequence: AK225965


    GeneLoc Exon Structure

    1 Ensembl transcript including schematic representation:
    ENST00000374561  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    ID3 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for ID3

    1 / 2 / 3

    3 probe-sets matching ID3 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    37043_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 AL021154 0.20 1.00 0.72 1

    207826_s_at2, 3 U133-A 1 1.00 1.00 -- -- NM_002167 0.60 1.00 0.82 1

    207826_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: AACCACTGCT

    SOURCE GeneReport for Unigene cluster: Hs.76884

    Expression variation in blood from EXPOLDB for ID3

    UniProtKB/Swiss-Prot: ID3_HUMAN, Q02535
    Tissue specificity: Expressed abundantly in lung, kidney and adrenal gland, but not in adult brain

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for ID3 gene from 5/6 species (see all 6 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    ID31   -- inhibitor of DNA binding 3, dominant negative helix-loop-helix more 92.16(n)
    99.16(a)
    403547  NM_001003025.1  NP_001003025.1 
    chimpanzee
    (Pan troglodytes)
    ID31   -- inhibitor of DNA binding 3, dominant negative helix-loop-helix more 99.44(n)
    99.16(a)
    745532  XM_001165695.1  XP_001165695.1 
    cow
    (Bos taurus)
    ID31   -- inhibitor of DNA binding 3, dominant negative helix-loop-helix more 91.6(n)
    97.48(a)
    538690  NM_001014950.1  NP_001014950.1 
    rat
    (Rattus norvegicus)
    Id31   -- inhibitor of DNA binding 3 87.96(n)
    97.48(a)
    25585  NM_013058.2  NP_037190.1 
    mouse
    (Mus musculus)
    Id31, 5 4 (66.00 cM)5
    inhibitor of DNA binding 31, 5 88.52(n)1
    96.64(a)1
    159031  NM_008321.11  NP_032347.11 
     AI1738235  AI8392835  (see all 22)
    About this table        Species with no ortholog for ID3

    ENSEMBL Gene Tree for ID3
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for ID3 gene
    ID12  ID22  ID42  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/56 NCBI SNPs in ID3 are shown (see all 56 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 39)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 1 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs115741,2
    A,C,F,H,O23758085(-) AGCTCG/ACTCCG 1 A/T mis111Minor allele frequency- A:0.15MN EU EA WA NA 1282
    rs29201,2
    A,C,F,H23757367(-) AGACTA/GAACCT 1 -- ut31 ese318Minor allele frequency- N:0.00MN EU EA WA NA 1776
    rs10500961,2
    A,C,F,H23757248(-) GGTCTT/CTTCAG 1 -- ut31 ese316Minor allele frequency- C:0.22MN EU EA WA NA 1546
    rs15550251,2
    A,C,F,H23759522(+) ATTGCG/TCTATT 1 -- ng3112Minor allele frequency- T:0.36NA EA MN EU WA 1266
    rs20714951,2
    C,F,H,O23756920(-) AACTTG/CCTTAT 1 -- ng5113Minor allele frequency- C:0.26EU EA WA NA 1154
    rs15550261,2
    C,F,H23759792(+) AATAGT/CTGCTT 1 -- ng317Minor allele frequency- C:0.05NA EA EU WA 650
    rs115423171,2
    C,F,H23758067(-) TCATCT/GCCAAC 1 A/S mis19Minor allele frequency- G:0.50EU EA WA NA 896
    rs27429481,2
    C,F,H23760774(+) ACTGCC/TTGGGG 1 -- ng31 tfbs34Minor allele frequency- T:0.01EU EA WA 414
    rs46490971,2
    C,F,H23760467(+) TAACCA/GAAGAG 1 -- ng31 trp315Minor allele frequency- G:0.44NA EU EA WA 1394
    rs20714941,2
    C,F,H23756956(-) CGCACA/GTGGCC 1 -- ng517Minor allele frequency- G:0.11NA EU EA WA 552
    About this table

    HapMap Linkage Disequilibrium images for ID3 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 600277

    7 Novoseek disease relationships for ID3 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    thyroid cancer 26.28 3 16394085 (2)
    leukemia t-cell 23.50 2 8632670 (2)
    lymphoma 15.20 2 15780199 (1), 8632670 (1)
    tumors 12.35 13 18069898 (2), 16394085 (2), 15342397 (2), 18048329 (1) (see all 6)
    retinoblastoma 7.87 2 12021231 (2)
    adenocarcinoma 0.00 4 11751402 (2), 11161400 (1)
    metastasis 0.00 1 15342397 (1)
    About this table

    1 PharmGKB disease relationship for ID3 gene
    Disease PharmGKB Relations PubMed IDs for articles supporting these relationships
    Leukemia, Lymphocytic, Acute, L1FA  GN  12086872
    About this table

    Genetic Association Database: ID3
    Human Genome Epidemiology Navigator: ID3 (2 documents)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/132 PubMed articles for ID3 gene (see all 132 ):
    (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, and/or H-InvDB)
    About This Section

    Entrez Gene: 3399 HGNC: 5362 AceView: ID3 Ensembl:ENSG00000117318 euGenes: HUgn3399
    ECgene: ID3 H-InvDB: ID3
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for ID3 Genetics and Cytogenetics in Oncology and Haematology
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for ID3:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for ID3 Antibodies for ID3
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for ID3 Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     shRNA in GFP-retroviral vector
     Search Tocris compounds for ID3




     Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
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