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

TTC39A Gene

protein-coding   GIFtS: 41
GCID: GC01M051752

tetratricopeptide repeat domain 39A

(Previous name: chromosome 1 open reading frame 34 )
(Previous symbol: C1orf34)
 Explore 2 diseases affiliated with
TTC39A via our new
 Human Malady Compendium 
Biological research products
for TTC39A
    

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

Aliases
Tetratricopeptide Repeat Domain 39A1 2     Differentially Expressed In MCF7 With Estradiol Protein 62 3
C1orf341 2 3     TPR Repeat Protein 39A2 3
DEME-61 2 3     Chromosome 1 Open Reading Frame 341
KIAA04521 3     Tetratricopeptide Repeat Protein 39A2

External Ids:    HGNC: 186571   Entrez Gene: 229962   Ensembl: ENSG000000858317   UniProtKB: Q5SRH93   

Export aliases for TTC39A gene to outside databases

Previous GC identifers: GC01M051526 GC01M049870


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

  --

(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_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TTC39A gene promoter:
         Tal-1   Pax-5   SREBP-1c   MyoD   LUN-1   c-Ets-1   SREBP-1b   SRY   SREBP-1a   RSRFC4   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for TTC39A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TTC39A


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

Entrez Gene cytogenetic band: 1p32.3   Ensembl cytogenetic band:  1p32.3   HGNC cytogenetic band: 1p32.3

TTC39A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TTC39A gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M051752:  view genomic region     (about GC identifiers)

Start:
51,752,930 bp from pter      End:
51,810,788 bp from pter
Size:
57,859 bases      Orientation:
minus 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: TT39A_HUMAN, Q5SRH9 (See protein sequence)
Recommended Name: Tetratricopeptide repeat protein 39A  
Size: 613 amino acids; 69778 Da
Sequence caution: Sequence=AAH28374.1; Type=Erroneous initiation; Sequence=BAA32297.1; Type=Erroneous initiation;
Note=Translation N-terminally shortened; Sequence=BAA32297.1; Type=Frameshift; Positions=373; Sequence=CAI13021.1;
Type=Erroneous gene model prediction; Sequence=CAI13022.1; Type=Erroneous gene model prediction; Sequence=CAI13023.1;
Type=Erroneous gene model prediction; Sequence=CAI13025.1; Type=Erroneous gene model prediction; Sequence=CAI13026.1;
Type=Erroneous gene model prediction; Sequence=CAI13027.1; Type=Erroneous gene model prediction; Sequence=CAI13131.1;
Type=Erroneous gene model prediction; Sequence=CAI13132.1; Type=Erroneous gene model prediction; Sequence=CAI13133.1;
Type=Erroneous gene model prediction; Sequence=CAI13135.1; Type=Erroneous gene model prediction; Sequence=CAI13136.1;
Type=Erroneous gene model prediction; Sequence=CAI13137.1; Type=Erroneous gene model prediction; Sequence=CAI13142.1;
Type=Erroneous gene model prediction;
Secondary accessions: O43417 O75040 Q5SRH5 Q5SRH6 Q5SRH7 Q5SRH8 Q5SRI0 Q5SRI1 Q5SRI2 Q5T7S1 Q6PIU8
Q9BT24
Alternative splicing: 4 isoforms:  Q5SRH9-1   Q5SRH9-2   Q5SRH9-3   Q5SRH9-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TTC39A: NX_Q5SRH9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q5SRH9

  • TTC39A Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001073963.1  NP_001138304.1  

    ENSEMBL proteins: 
     ENSP00000431228   ENSP00000393952   ENSP00000406144   ENSP00000262675   ENSP00000360815  
     ENSP00000436659   ENSP00000360812   ENSP00000262676   ENSP00000408532   ENSP00000405803  
     ENSP00000388995   ENSP00000370230   ENSP00000383830   ENSP00000434483   ENSP00000432453  
     ENSP00000397207  

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    Uscn Proteins for TTC39A

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--


    TTC39A for ontologies           About GeneDecksing



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

    TTC39A for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR011990 TPR-like_helical
     IPR019412 OMP_IML2_mit/TPR_39
     IPR019734 TPR_repeat

    Graphical View of Domain Structure for InterPro Entry Q5SRH9

    ProtoNet protein and cluster: Q5SRH9

    UniProtKB/Swiss-Prot: TT39A_HUMAN, Q5SRH9
    Similarity: Belongs to the TTC39 family
    Similarity: Contains 3 TPR repeats


    (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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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TTC39A

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--


    TTC39A for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for TTC39A:
     Synthetic lethal with Ras 


    (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 TTC39A

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for TTC39A (ENSP000004061444) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    --ENSP000004058564STRING: ENSP00000405856
    --ENSP000003919584STRING: ENSP00000391958
    --ENSP000003938644STRING: ENSP00000393864
    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:0008150biological_process ND--


    TTC39A 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 TTC39A
    Search CenterWatch for drugs/clinical trials and news about TTC39A / TT39A 

    (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 TTC39A gene (2 alternative transcripts): 
    NM_001080494.2  NM_001144832.1  

    Unigene Cluster for TTC39A:

    Tetratricopeptide repeat domain 39A
    Hs.112949  [show with all ESTs]
    Unigene Representative Sequence: AB007921
    18/19 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 19):
    ENST00000530004(uc001csj.3) ENST00000447632(uc001csk.3 uc001csl.3)
    ENST00000413473(uc010ond.2 uc010one.2 uc010onf.2) ENST00000262675
    ENST00000371750 ENST00000534098 ENST00000525906 ENST00000431927 ENST00000371747(uc001csn.3 uc009vyy.1)
    ENST00000262676(uc001cso.1) ENST00000524442 ENST00000411642 ENST00000439482
    ENST00000422925 ENST00000380849 ENST00000401051 ENST00000532836 ENST00000527205


    miRNA
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    8/32 QIAGEN miScript miRNA Assays for microRNAs that regulate TTC39A (see all 32):
    hsa-miR-485-3p hsa-miR-128 hsa-miR-30d hsa-miR-30a hsa-miR-28-5p hsa-miR-181b hsa-miR-203 hsa-miR-99b
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    Additional cDNA sequence: 

    AB007921.1 AF007170.1 AK000220.1 AK298019.1 AK301587.1 AK311430.1 BC004399.1 BC028374.2 

    13 DOTS entries:

    DT.92420944  DT.100020705  DT.99989507  DT.97839415  DT.95263967  DT.95263969  DT.101977460  DT.95278892 
    DT.92065811  DT.95119630  DT.100745828  DT.86854941  DT.40122030 

    24/91 AceView cDNA sequences (see all 91):

    BU541148 BE407151 AI659827 BM554142 BU556547 AI951064 AW663931 BI761577 
    BM800775 AF007170 AI916581 AK000220 BC004399 BM793951 AA506764 BM844716 
    BM852537 BM459065 BQ943557 BM924382 BQ069308 BI820738 BQ223110 AL045212 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for TTC39A (see all 7)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21 ^
    SP1:                                                                                                  -           -     -           -                           
    SP2:                                                  -                                               -           -     -           -                           
    SP3:              -     -                                                                             -           -     -                                       
    SP4:        -     -     -                                                                                                                                       
    SP5:                    -                                                                                                                                       

    ExUns: 22a · 22b · 22c
    SP1:                  
    SP2:                  
    SP3:                  
    SP4:                  
    SP5:                  


    ECgene alternative splicing isoforms for TTC39A

    (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

    TTC39A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

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

    About this image
    See TTC39A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TTC39A

    SOURCE GeneReport for Unigene cluster: Hs.112949
        SABiosciences Custom PCR Arrays for TTC39A
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TTC39A

    (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 TTC39A gene from 6/20 species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves TTC39A1 tetratricopeptide repeat domain 39A 70.61(n)
    76(a)
      424632  XM_422466.3  XP_422466.3 
    lizard
    (Anolis carolinensis)
    Reptilia TTC39A6
    --
    65(a)
    1 ↔ 1
    2(77855054-77878647)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.95182 Transcribed sequence with weak similarity to protein more 76.63(n)    BX762425.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ttc39a1 tetratricopeptide repeat domain 39A 67.73(n)
    69.4(a)
      100320357  XM_002663097.1  XP_002663143.1 
    honey bee
    (Apis mellifera)
    Insecta --
    --
    36(a)
    1 → many
    Group2.1(172506-175367)
    worm
    (Caenorhabditis elegans)
    Secernentea C32D5.66
    Uncharacterized protein C32D5.6
    35(a)
    1 → many
    II(6331870-6333955)


    ENSEMBL Gene Tree for TTC39A (if available)
    TreeFam Gene Tree for TTC39A (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TTC39A gene
    TTC39B2  TTC39C2  
    1 SIMAP similar gene for TTC39A using alignment to 9 protein entries:     TT39A_HUMAN (see all proteins):
    TTC39B

    TTC39A 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

    10/903 NCBI SNPs in TTC39A are shown (see all 903    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1888758201,2
    --51752431(+) CCCTAC/TGGGGA 2 -- int10--------
    rs1921904361,2
    --51752484(+) AAAACA/CTGGTG 2 -- int10--------
    rs127236251,2
    C,H--51752529(+) CCTAGA/TGGTTG 2 -- int14Minor allele frequency- T:0.00NS EA 418
    rs1838160031,2
    --51752612(+) ATTGTC/TGCCTC 2 -- int10--------
    rs1896105961,2
    --51752620(+) CTCATA/GGGAAT 2 -- int10--------
    rs1815708041,2
    --51752633(+) GGCTCA/CATGTT 2 -- int10--------
    rs1454585981,2
    --51752775(+) AGGCCA/GTGTGG 2 -- int10--------
    rs1472331201,2
    --51752851(+) ATGCAC/TGATCC 2 -- int10--------
    rs1407371271,2
    --51752904(+) TAACTC/GAAGAA 2 -- int10--------
    rs75314561,2
    C,F,A,--51752916(+) CTAACG/ACATAC 2 -- int113Minor allele frequency- A:0.23NA WA CSA EA 554

    HapMap Linkage Disequilibrium report for TTC39A (51752930 - 51810788 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for TTC39A: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing TTC39A
    DNA2.0 Custom Variant and Variant Library Synthesis for TTC39A

    (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

    TTC39A for disorders           About GeneDecksing

    2 diseases for TTC39A:    About MalaCards
    breast carcinoma    carcinoma


    Export disorders for TTC39A 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 TTC39A gene integrated from 9 sources:
    (articles sorted by number of sources associating them with TTC39A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Differential screening and suppression subtractive hybridization identified genes differentially expressed in an estrogen receptor- positive breast carcinoma cell line. (PubMed id 9461476)1, 2, 3 Kuang W.W.... Weigel R.J. (1998)
    2. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. (PubMed id 9455484)1, 2, 3 Seki N.... Ohara O. (1997)
    3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (2006)
    4. 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)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
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      (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)
    About This Section
    Entrez Gene: 22996 HGNC: 18657 AceView: C1orf34 Ensembl:ENSG00000085831 euGenes: HUgn22996
    ECgene: TTC39A H-InvDB: TTC39A

    (According to HUGE)
    About This Section
    HUGE: KIAA0452

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for TTC39A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for TTC39A gene:
    Search GeneIP for patents involving TTC39A

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



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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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