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GTF2H2 Gene

protein-coding   GIFtS: 63
GCID: GC05M070330

General Transcription Factor IIH, Polypeptide 2, 44kDa

(Previous names: general transcription factor IIH, polypeptide 2 (44kD subunit))
  See GTF2H2-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
General Transcription Factor IIH, Polypeptide 2, 44kDa1 2     BTF22
Basic Transcription Factor 2 44 KDa Subunit2 3     T-BTF2P442
General Transcription Factor IIH Polypeptide 22 3     TFIIH2
BTF2P442 3     General Transcription Factor IIH Subunit 22
BTF2 P442 3     General Transcription Factor IIH, Polypeptide 2, 44kD Subunit2
TFIIH Basal Transcription Factor Complex P44 Subunit2 3     p442
General Transcription Factor IIH, Polypeptide 2 (44kD Subunit)1     

External Ids:    HGNC: 46561   Entrez Gene: 29662   Ensembl: ENSG000001457367   OMIM: 6017485   UniProtKB: Q138883   

Export aliases for GTF2H2 gene to outside databases

Previous GC identifers: GC05P069008 GC05P070422 GC05P068962 GC05M070366 GC05P065807


(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 GTF2H2 Gene:
This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least
four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and
complexity of the sequence have also caused difficulty in determining the organization of this genomic region.
This gene is within the telomeric copy of the duplication. Deletion of this gene sometimes accompanies deletion
of the neighboring SMN1 gene in spinal muscular atrophy (SMA) patients but it is unclear if deletion of this gene
contributes to the SMA phenotype. This gene encodes the 44 kDa subunit of RNA polymerase II transcription
initiation factor IIH which is involved in basal transcription and nucleotide excision repair. Transcript
variants for this gene have been described, but their full length nature has not been determined. A second copy
of this gene within the centromeric copy of the duplication has been described in the literature. It is reported
to be different by either two or four base pairs; however, no sequence data is currently available for the
centromeric copy of the gene. (provided by RefSeq, Jul 2008)

GeneCards Summary for GTF2H2 Gene:
GTF2H2 (general transcription factor IIH, polypeptide 2, 44kDa) is a protein-coding gene. Diseases associated with GTF2H2 include werdnig-hoffmann disease, and seminoma. GO annotations related to this gene include protein kinase activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is GTF2H2C.

UniProtKB/Swiss-Prot: TF2H2_HUMAN, Q13888
Function: Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of
DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. The N-terminus interacts with and
regulates XPD whereas an intact C-terminus is required for a successful escape of RNAP II form the promoter

Gene Wiki entry for GTF2H2 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_000005.9  NT_034772.7  NT_187651.1  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the GTF2H2 gene promoter:
         Sox5   POU6F1 (c2)   Cdc5   NF-kappaB   HNF-4alpha1   POU2F1   POU2F1a   NF-kappaB2   Cart-1   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): GTF2H2 promoter sequence
   Search Chromatin IP Primers for GTF2H2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat GTF2H2


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

Entrez Gene cytogenetic band: 5q13.2   Ensembl cytogenetic band:  5q13.2   HGNC cytogenetic band: 5q13.2

GTF2H2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
GTF2H2 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M070330:  view genomic region     (about GC identifiers)

Start:
70,330,784 bp from pter      End:
70,363,516 bp from pter
Size:
32,733 bases      Orientation:
minus strand

1 alternative location:
Chr5-,NW_003315917.2 965,419-997,916     

(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, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: TF2H2_HUMAN, Q13888 (See protein sequence)
Recommended Name: General transcription factor IIH subunit 2  
Size: 395 amino acids; 44419 Da
Subunit: One of the 6 subunits forming the core-TFIIH basal transcription factor which associates with the CAK
complex composed of CDK7, CCNH/cyclin H and MNAT1 to form the TFIIH basal transcription factor. Interacts with
XPB, XPD, GTF2H1 and GTF2H3. Interacts with varicella-zoster virus IE63 protein
1 PDB 3D structure from and Proteopedia for GTF2H2:
1Z60 (3D)    
Secondary accessions: Q15570 Q15571 Q9BS41
Alternative splicing: 1 isoform:  Q13888-1   

Explore the universe of human proteins at neXtProt for GTF2H2: NX_Q13888

Explore proteomics data for GTF2H2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys23, Lys116
  • Modification sites at PhosphoSitePlus

  • See GTF2H2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001506.1  
    ENSEMBL proteins: 
     ENSP00000274400   ENSP00000428718   ENSP00000328901   ENSP00000473333   ENSP00000429057  
     ENSP00000473362   ENSP00000394164  
    Reactome Protein details: Q13888

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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:
    TFIIH: General transcription factor IIH complex subunits
    GTF: General transcription factors

    5 InterPro protein domains:
     IPR012170 TFIIH_SSL1/p44
     IPR007198 Ssl1-like
     IPR007087 Znf_C2H2
     IPR004595 TFIIH_C1-like_dom
     IPR002035 VWF_A

    Graphical View of Domain Structure for InterPro Entry Q13888

    ProtoNet protein and cluster: Q13888

    2 Blocks protein domains:
    IPB001841 Zn-finger
    IPB007198 Ssl1-like


    UniProtKB/Swiss-Prot: TF2H2_HUMAN, Q13888
    Similarity: Belongs to the GTF2H2 family
    Similarity: Contains 1 VWFA domain


    Find genes that share domains with GTF2H2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: TF2H2_HUMAN, Q13888
    Function: Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of
    DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. The N-terminus interacts with and
    regulates XPD whereas an intact C-terminus is required for a successful escape of RNAP II form the promoter

         Gene Ontology (GO): Selected molecular function terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding TAS8194529
    GO:0003700sequence-specific DNA binding transcription factor activity NAS8194529
    GO:0004672contributes to protein kinase activity IDA9852112
    GO:0005515protein binding IPI11445587
    GO:0008094contributes to DNA-dependent ATPase activity IDA9852112
         
    Find genes that share ontologies with GTF2H2           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for GTF2H2

    miRNA
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    miRTarBase miRNAs that target GTF2H2:
    hsa-mir-122-5p (MIRT023302), hsa-mir-324-3p (MIRT042884), hsa-mir-30a-5p (MIRT028505)

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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
    TF2H2_HUMAN, Q13888: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000439core TFIIH complex IEA--
    GO:0005654nucleoplasm TAS--
    GO:0005675holo TFIIH complex IDA9852112

    Find genes that share ontologies with GTF2H2           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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    SuperPaths for GTF2H2 About   (see all 18)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1Global Genomic NER (GG-NER)
    Global Genomic NER (GG-NER)0.69
    Formation of incision complex in GG-NER0.62
    Nucleotide excision repair0.69
    Nucleotide Excision Repair Pathway0.48
    Dual incision reaction in GG-NER0.62
    2Formation of RNA Pol II elongation complex
    mRNA Capping0.93
    RNA Polymerase II Pre-transcription Events0.73
    RNA Pol II CTD phosphorylation and interaction with CE0.93
    Transcription of the HIV genome0.71
    RNA Pol II CTD phosphorylation and interaction with CE0.93
    RNA Polymerase II Transcription Initiation And Promoter Clearance0.67
    Formation of the Early Elongation Complex0.77
    RNA Polymerase II Transcription Initiation0.67
    3Assembly of RNA Polymerase-II Initiation Complex
    Assembly of RNA Polymerase-II Initiation Complex0.91
    Basal transcription factors0.50
    Transcription of mRNA0.91
    Crosstalk Between CARM1 and ESRs0.39
    Protein Acetylation and Deacetylation0.51
    4DNA Repair
    Transcription-coupled NER (TC-NER)0.90
    Formation of transcription-coupled NER (TC-NER) repair complex0.65
    Nucleotide Excision Repair0.90
    DNA Repair0.45
    Dual incision reaction in TC-NER0.65
    5RNA Polymerase I Promoter Opening
    RNA Polymerase I Transcription0.78
    RNA Polymerase I Promoter Clearance0.78
    RNA Polymerase I Chain Elongation0.78
    RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription0.73


    Find genes that share SuperPaths with GTF2H2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for GTF2H2 (see all 11)
        Nuclear Receptor Activation by Vitamin-A
    Protein Acetylation and Deacetylation
    Androgen Signaling
    Nucleotide Excision Repair Pathway
    Glucocorticoid Receptor Signaling

    2 GeneGo (Thomson Reuters) Pathways for GTF2H2
        Transcription P53 signaling pathway
    Transcription Ligand-Dependent Transcription of Retinoid-Target genes

    2 BioSystems Pathways for GTF2H2
        Eukaryotic Transcription Initiation
    Validated targets of C-MYC transcriptional repression

    Selected Reactome Pathways for GTF2H2 (see all 27)
        Formation of RNA Pol II elongation complex
    Tat-mediated elongation of the HIV-1 transcript
    RNA Polymerase I Promoter Escape
    NoRC negatively regulates rRNA expression
    RNA Polymerase II Transcription Initiation And Promoter Clearance


    3 Kegg Pathways  (Kegg details for GTF2H2):
        Basal transcription factors
    Nucleotide excision repair
    Viral carcinogenesis

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for GTF2H2
    Interactions:

        GeneGlobe Interaction Network for GTF2H2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for GTF2H2 (Q138883 ENSP000002744004) via UniProtKB, MINT, STRING, and/or I2D (see all 44)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000233149Q927593, ENSP000003954974I2D: score=1 STRING: ENSP00000395497
    GTF2H4Q927593, ENSP000002598954I2D: score=1 STRING: ENSP00000259895
    ENSG00000236895Q927593, ENSP000003962514I2D: score=1 STRING: ENSP00000396251
    ENSG00000221974Q927593I2D: score=1 
    ENSG00000226384Q927593I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 21):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000718nucleotide-excision repair, DNA damage removal TAS--
    GO:0002031G-protein coupled receptor internalization IMP15775968
    GO:0006200ATP catabolic process IDA9852112
    GO:0006281DNA repair TAS--
    GO:0006283transcription-coupled nucleotide-excision repair TAS--

    Find genes that share ontologies with GTF2H2           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 GTF2H2 (TF2H2)

    3 Novoseek inferred chemical compound relationships for GTF2H2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    zinc 2.43 2 8194529 (1), 10882739 (1)
    atp 0 2 11141066 (1), 11089979 (1)
    cisplatin 0 2 11600136 (1)



    Find genes that share compounds with GTF2H2           About GenesLikeMe



    (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 GTF2H2 gene: 
    NM_001515.3  

    Unigene Cluster for GTF2H2:

    General transcription factor IIH, polypeptide 2, 44kDa
    Hs.607501  [show with all ESTs]
    Unigene Representative Sequence: BX647532
    14 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000274400 ENST00000519783 ENST00000330280(uc003kav.4 uc003kau.4 uc011crt.2)
    ENST00000518898 ENST00000517900 ENST00000521942 ENST00000522654 ENST00000523003(uc003kay.1)
    ENST00000521858(uc003kaz.3) ENST00000523693 ENST00000508592 ENST00000521602
    ENST00000518275 ENST00000425596
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    Additional mRNA sequence: 

    AF078847.1 AF086359.1 AK296578.1 BC005345.1 BC171919.1 BT006773.1 BX537982.1 BX647532.1 
    DQ786239.1 DQ786268.1 NR_033417.1 U21910.1 U21915.1 Z30094.1 

    Selected DOTS entries (see all 35):

    DT.102840497  DT.95199285  DT.120845171  DT.413008  DT.120845156  DT.429771  DT.102833003  DT.100822315 
    DT.100822322  DT.120845041  DT.214322  DT.75143754  DT.100026778  DT.120845251  DT.427316  DT.91719169 
    DT.100822319  DT.100822320  DT.100822324  DT.100822329  DT.100822331  DT.120845005  DT.92399188  DT.97844340 

    Selected AceView cDNA sequences (see all 273):

    BU625514 BQ030091 BI054485 AI571315 AI056697 AA306816 AA293389 AI625149 
    AI472627 BU172664 AA829390 N72406 AI205195 BX279649 AA639150 AA989156 
    AA678043 BM768623 BM462360 AW803619 BG169070 AW592525 BQ182999 W19716 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for GTF2H2 (see all 8)    About this scheme

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


    ECgene alternative splicing isoforms for GTF2H2

    (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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    GTF2H2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    GTF2H2 Expression
    About this image

    GTF2H2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    GTF2H2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.607501

    UniProtKB/Swiss-Prot: TF2H2_HUMAN, Q13888
    Tissue specificity: Widely expressed, with higher expression in skeletal muscle

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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 eukaryotes.

    Orthologs for GTF2H2 gene from Selected species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Gtf2h21 , 5 general transcription factor II H, polypeptide 21, 5 90.72(n)1
    97.22(a)1
      13 (53.21 cM)5
    238941  NM_022011.41  NP_071294.31 
     1004602185 
    chicken
    (Gallus gallus)
    Aves GTF2H21 general transcription factor IIH, polypeptide 2, 44kDa 79.07(n)
    88.35(a)
      100858972  XM_003643075.2  XP_003643123.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    82(a)
    1 → many
    2(16892487-16947416)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.66062 Transcribed sequence with moderate similarity to protein more 78.02(n)    CF220859.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.16302 Danio rerio mRNA similar to general transcription factor more 75.59(n)    BC045397.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Ssl11 , 3 transcription initiation from Pol II
    promoter more3
    Ssl11
    50(a)3
    53.06(n)1
    53.06(a)1
      80B23
    405091  NM_001275298.11  NP_001262227.11 
    worm
    (Caenorhabditis elegans)
    Secernentea T16H12.43
    CELE_T16H12.41
    transcription factor IIH subunit3
    CELE_T16H12.41
    42(a)3
    52.47(n)1
    45.28(a)1
      III(10160514-10162439)3
    1764211  NM_066838.31  NP_499239.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SSL1(YLR005W)4
    SSL11
    Component of the core form of RNA polymerase transcription more4
    SSL11
    49.18(n)1
    42.08(a)1
      12(160049-161434)4
    8506911, 4  NP_013105.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons GTF2H21 GTF2H2 49.29(n)
    45.99(a)
      839332  NM_148434.3  NP_683275.2 
    rice
    (Oryza sativa)
    Liliopsida Os04g05089001 Os04g0508900 50.99(n)
    43.71(a)
      4336358  NM_001059809.2  NP_001053274.2 


    ENSEMBL Gene Tree for GTF2H2 (if available)
    TreeFam Gene Tree for GTF2H2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for GTF2H2 gene
    GTF2H2C2  
    2 SIMAP similar genes for GTF2H2 using alignment to 4 protein entries:     TF2H2_HUMAN (see all proteins):
    GTF2H2D    GTF2H2C

    Find genes that share paralogs with GTF2H2           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for GTF2H2
    PGOHUM00000257105


    (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 GTF2H2 (see all 39)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1899953991,2
    --70330806(+) TGAGAG/TGGAGT 1 -- ds50010--------
    rs1825362531,2
    C--70330845(+) AATCTC/TGGCTC 1 -- ds50010--------
    rs1866230881,2
    --70331880(+) TCAATC/TATTTC 1 -- int10--------
    rs5628781,2
    C--70332181(+) CTTCAC/TACACA 1 -- int10--------
    rs1928094541,2
    --70333840(+) TAATTA/TAAAAA 1 -- int10--------
    rs1837878321,2
    --70334234(+) TCTAAC/TGTTTG 1 -- int10--------
    rs1891990291,2
    --70334255(+) ACTTAC/TTCTAA 1 -- int10--------
    rs1997811911,2
    --70338021(+) TTACAC/TTCAAC 2 E syn10--------
    rs1394083401,2
    --70340864(+) ATCACC/TTAATG 1 -- int10--------
    rs1931162231,2
    --70341748(+) GCTATA/CTATTT 1 -- int10--------

    HapMap Linkage Disequilibrium report for GTF2H2 (70330784 - 70363516 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for GTF2H2 (see all 55):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2673843CNV Deletion23128226
    dgv6149n71CNV Loss21882294
    dgv27n14CNV Loss18776910
    nsv881768CNV Loss21882294
    dgv6170n71CNV Loss21882294
    nsv882034CNV Loss21882294
    nsv821643CNV Loss15273396
    dgv6135n71CNV Loss21882294
    dgv6136n71CNV Loss21882294
    dgv6168n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing GTF2H2
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601748    OMIM disorders: --

    4 diseases for GTF2H2:    
    About MalaCards
    werdnig-hoffmann disease    seminoma    muscular atrophy    idiopathic pulmonary fibrosis

    1 disease from the University of Copenhagen DISEASES database for GTF2H2:
    Muscular atrophy

    Find genes that share disorders with GTF2H2           About GenesLikeMe

    5 Novoseek inferred disease relationships for GTF2H2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    muscular atrophy spinal 78.5 11 17903057 (1), 10673506 (1), 10686493 (1)
    werdnig-hoffmann disease 63.9 1 8981949 (1)
    cockayne syndrome 61.9 1 8652557 (1)
    xeroderma pigmentosum 54.7 1 8652557 (1)
    genetic disorder 23 2 14550632 (1), 20016270 (1)

    Genetic Association Database (GAD): GTF2H2
    Human Genome Epidemiology (HuGE) Navigator: GTF2H2 (1 document)

    Export disorders for GTF2H2 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 GTF2H2 gene, integrated from 10 sources (see all 137):
    (articles sorted by number of sources associating them with GTF2H2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. p44 and p34 subunits of the BTF2/TFIIH transcription factor have homologies with SSL1, a yeast protein involved in DNA repair. (PubMed id 8194529)1, 2, 3, 9 Humbert S....Moncollin V. (EMBO J. 1994)
    2. A multicopy transcription-repair gene, BTF2p44, maps to the SMA region and demonstrates SMA associated deletions. (PubMed id 9063743)1, 2, 9 Carter T.A.... Gilliam T.C. (Hum. Mol. Genet. 1997)
    3. A population-based study of genotypic and phenotypic variability in children with spinal muscular atrophy. (PubMed id 19154529)1, 4, 9 Arkblad E....Darin N. (Acta Paediatr. 2009)
    4. 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)
    5. A role of the C-terminal part of p44 in the promoter escape activity of transcription factor IIH. (PubMed id 11319235)1, 2 Tremeau-Bravard A.... Egly J.-M. (J. Biol. Chem. 2001)
    6. Sequence of a 131-kb region of 5q13.1 containing the spinal muscular atrophy candidate genes SMN and NAIP. (PubMed id 9503025)1, 2 Chen Q....MacKenzie A.E. (Genomics 1998)
    7. Immunoaffinity purification and functional characterization of human transcription factor IIH and RNA polymerase II from clonal cell lines that conditionally express epitope-tagged subunits of the multiprotein complexes. (PubMed id 9852112)1, 2 Kershnar E.... Chiang C.-M. (J. Biol. Chem. 1998)
    8. A provisional transcript map of the spinal muscular atrophy (SMA) critical region. (PubMed id 7552146)1, 2 van der Steege G.... Buys C.H.C.M. (Eur. J. Hum. Genet. 1995)
    9. Substrate specificity of the cdk-activating kinase (CAK) is altered upon association with TFIIH. (PubMed id 9130708)1, 9 Rossignol M....Egly J.M. (EMBO J. 1997)
    10. Interactions involving the human RNA polymerase II transcription/nucleotide excision repair complex TFIIH, the nucleotide excision repair protein XPG, and Cockayne syndrome group B (CSB) protein. (PubMed id 8652557)1, 9 Iyer N....Friedberg E.C. (Biochemistry 1996)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 2966 HGNC: 4656 AceView: GTF2H2.2 Ensembl:ENSG00000145736 euGenes: HUgn2966
    ECgene: GTF2H2 Kegg: 2966 H-InvDB: GTF2H2

    (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 GTF2H2 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for GTF2H2 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 GTF2H2 gene:
    Search GeneIP for patents involving GTF2H2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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