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TTC9B Gene

protein-coding   GIFtS: 43
GCID: GC19M040721

Tetratricopeptide Repeat Domain 9B

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Tetratricopeptide Repeat Domain 9B1 2
TPR Repeat Protein 9B2 3
Tetratricopeptide Repeat Protein 9B2

External Ids:    HGNC: 263951   Entrez Gene: 1480142   Ensembl: ENSG000001745217   UniProtKB: Q8N6N23   

Export aliases for TTC9B gene to outside databases

Previous GC identifers: GC19M045417 GC19M037156


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TTC9B Gene:
TTC9B (tetratricopeptide repeat domain 9B) is a protein-coding gene. An important paralog of this gene is TTC9C.


(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_000019.9  NC_018930.2  NT_011109.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the TTC9B gene promoter:
         NF-1   HOXA5   NRSF form 1   Pax-4a   NRSF form 2   YY1   Roaz   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTTC9B promoter sequence
   Search Chromatin IP Primers for TTC9B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TTC9B


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

Entrez Gene cytogenetic band: 19q13.2   Ensembl cytogenetic band:  19q13.2   HGNC cytogenetic band: 19q13.2

TTC9B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TTC9B gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M040721:  view genomic region     (about GC identifiers)

Start:
40,721,965 bp from pter      End:
40,724,306 bp from pter
Size:
2,342 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., 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: TTC9B_HUMAN, Q8N6N2 (See protein sequence)
Recommended Name: Tetratricopeptide repeat protein 9B  
Size: 239 amino acids; 25932 Da
Secondary accessions: A8K0I5 Q96NP9
Alternative splicing: 2 isoforms:  Q8N6N2-1   Q8N6N2-2   (No experimental confirmation available. May be due to an intron retention)

Explore the universe of human proteins at neXtProt for TTC9B: NX_Q8N6N2

Explore proteomics data for TTC9B at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See TTC9B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689692.2  
    ENSEMBL proteins: 
     ENSP00000311760  

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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:
    TTC: Tetratricopeptide (TTC) repeat domain containing

    5 InterPro protein domains:
     IPR011990 TPR-like_helical
     IPR023566 PPIase_FKBP
     IPR013105 TPR_2
     IPR013026 TPR-contain_dom
     IPR019734 TPR_repeat

    Graphical View of Domain Structure for InterPro Entry Q8N6N2

    ProtoNet protein and cluster: Q8N6N2

    UniProtKB/Swiss-Prot: TTC9B_HUMAN, Q8N6N2
    Similarity: Belongs to the TTC9 family
    Similarity: Contains 2 TPR repeats


    Find genes that share domains with TTC9B           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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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005515protein binding ----
         
    Find genes that share ontologies with TTC9B           About GenesLikeMe


    Animal Models:
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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 COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    mitochondrion2
    extracellular1
    nucleus1

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

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

    Find genes that share ontologies with TTC9B           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TTC9B
    Interactions:

        Search GeneGlobe Interaction Network for TTC9B

    1 Interacting protein for TTC9B (Q8N6N23) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GRID2O434243I2D: score=1 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    Find genes that share ontologies with TTC9B           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
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      Browse compounds at ApexBio 

    Browse Tocris compounds for TTC9B



    (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 TTC9B gene: 
    NM_152479.5  

    Unigene Cluster for TTC9B:

    Tetratricopeptide repeat domain 9B
    Hs.631572  [show with all ESTs]
    Unigene Representative Sequence: BX329490
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000311308(uc002onc.3) ENST00000593586
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      QuantiTect SYBR Green Assays in human, mouse, rat TTC9B
      QuantiFast Probe-based Assays in human, mouse, rat TTC9B

    Additional mRNA sequence: 

    AK289550.1 BC029539.1 

    2 DOTS entries:

    DT.75167501  DT.435357 

    Selected AceView cDNA sequences (see all 50):

    AW294006 AK054935 BX438002 CR610812 AW298160 BI488440 CR626768 AI936647 
    CR596147 BX394003 AW160639 CR617938 AA338626 AI598178 BX454905 AA338625 
    BM676619 BI819499 CA432622 BC029539 AL530363 BX281141 NM_152479 BU620981 

    GeneLoc Exon Structure


    (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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    TTC9B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTTTGTTGG
    TTC9B Expression
    About this image


    TTC9B expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Endothelium (Cardiovascular System)
             Endothelial Cells Blood Brain Barrier
     
     Brain (Nervous System)
             Endothelial Cells Blood Brain Barrier
    TTC9B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TTC9B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.631572
        Custom PCR Arrays for TTC9B
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for TTC9B gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ttc9b1 , 5 tetratricopeptide repeat domain 9B1, 5 89.03(n)1
    91.98(a)1
      7 (15.95 cM)5
    730321  NM_028417.11  NP_082693.11 
     276539155 
    lizard
    (Anolis carolinensis)
    Reptilia TTC9B6
    tetratricopeptide repeat domain 9B
    67(a)
    1 ↔ 1
    LGf(2366962-2368024)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia ttc9b1 tetratricopeptide repeat domain 9B 64.47(n)
    65.93(a)
      779712  NM_001078791.2  NP_001072259.2 
    zebrafish
    (Danio rerio)
    Actinopterygii ttc9b1 tetratricopeptide repeat domain 9B 68.44(n)
    69.82(a)
      559732  NM_001044905.2  NP_001038370.1 


    ENSEMBL Gene Tree for TTC9B (if available)
    TreeFam Gene Tree for TTC9B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TTC9B gene
    TTC9C2  TTC92  
    2 SIMAP similar genes for TTC9B using alignment to 1 protein entry:     TTC9B_HUMAN:
    TTC9C    TTC9

    Find genes that share paralogs with TTC9B           About GenesLikeMe



    (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 TTC9B (see all 76)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2022468521,2
    --40722109(+) CCACTA/GTCTTC 2 D syn10--------
    rs115534641,2,,4
    C,H--40722122(+) GCTGGA/GGGCTG 2 P L mis1 ese36Minor allele frequency- G:0.00NS EA NA 410
    rs1417682071,2
    --40722377(+) TGTGCA/GCCTGT 1 -- int10--------
    rs1470548561,2
    --40722385(+) TGTATA/TTGCGG 1 -- int10--------
    rs1452176471,2
    C--40722626(+) GCACG-/CACACAC 1 -- int10--------
    rs81083511,2
    C,H--40722659(+) CATCGC/TCCACC 1 -- int113Minor allele frequency- T:0.01NA WA CSA EA 378
    rs1929626211,2
    --40722837(+) ATGACA/GGTAGA 1 -- int10--------
    rs557108491,2
    C,F--40722927(+) ATGGAC/TGAGTG 1 -- int16Minor allele frequency- T:0.49NA WA EA 248
    rs747243111,2
    C,F--40723001(+) CTGCTA/GTTCTG 1 -- int12Minor allele frequency- G:0.05CSA WA 120
    rs2009560541,2
    C--40723048(+) CTTTCC/GCCGCC 1 -- int10--------

    HapMap Linkage Disequilibrium report for TTC9B (40721965 - 40724306 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for TTC9B:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv911699CNV Loss21882294
    dgv3865n71CNV Loss21882294
    dgv3866n71CNV Loss21882294
    nsv9728CNV Loss18304495
    dgv1083e1CNV Complex17122850

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (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 TTC9B gene integrated from 10 sources:
    (articles sorted by number of sources associating them with TTC9B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)
    3. 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. (Genome Res. 2004)
    4. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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, Kegg, and/or H-InvDB)
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    Entrez Gene: 148014 HGNC: 26395 AceView: MGC33962 Ensembl:ENSG00000174521 euGenes: HUgn148014
    ECgene: TTC9B H-InvDB: TTC9B

    (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 TTC9B Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for TTC9B gene:
    Search GeneIP for patents involving TTC9B

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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