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TSSC1 Gene

protein-coding   GIFtS: 52
GCID: GC02M003171

Tumor Suppressing Subtransferable Candidate 1

  See TSSC1-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
Tumor Suppressing Subtransferable Candidate 11 2
Tumor-Suppressing STF CDNA 1 Protein2 3
Tumor-Suppressing Subchromosomal Transferable Fragment Candidate Gene 1
Protein2 3
Protein TSSC12

External Ids:    HGNC: 123831   Entrez Gene: 72602   Ensembl: ENSG000000323897   OMIM: 6089985   UniProtKB: Q53HC93   

Export aliases for TSSC1 gene to outside databases

Previous GC identifers: GC02M004586 GC02M004873 GC02M004802 GC02M004731


(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 TSSC1 Gene:
This gene has been reported in PMID 9403053 as one of several tumor-suppressing subtransferable fragments located
in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region
have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical
carcinoma, and lung, ovarian, and breast cancer. Alignment of this gene to genomic sequence data suggests that
this gene resides on chromosome 2 rather than chromosome 11. (provided by RefSeq, Dec 2008)

GeneCards Summary for TSSC1 Gene:
TSSC1 (tumor suppressing subtransferable candidate 1) is a protein-coding gene. Diseases associated with TSSC1 include wilms tumor, and breast cancer.

Gene Wiki entry for TSSC1 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_000002.11  NT_005334.17  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TSSC1 gene promoter:
         NF-YA   HSF1 (long)   CBF-C   Arnt   Max   HSF1short   CP1A   CP1C   NF-Y   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): TSSC1 promoter sequence
   Search Chromatin IP Primers for TSSC1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TSSC1


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

Entrez Gene cytogenetic band: 2p25.3   Ensembl cytogenetic band:  2p25.3   HGNC cytogenetic band: 2p25.3

TSSC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TSSC1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M003171:  view genomic region     (about GC identifiers)

Start:
3,192,696 bp from pter      End:
3,381,653 bp from pter
Size:
188,958 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: TSSC1_HUMAN, Q53HC9 (See protein sequence)
Recommended Name: Protein TSSC1  
Size: 387 amino acids; 43603 Da
Secondary accessions: D6W4Y1 O43179 Q53S19 Q53SG2

Explore the universe of human proteins at neXtProt for TSSC1: NX_Q53HC9

Explore proteomics data for TSSC1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys91, Lys240, Lys382
  • Modification sites at PhosphoSitePlus

  • See TSSC1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_003301.1  
    ENSEMBL proteins: 
     ENSP00000381652   ENSP00000371559   ENSP00000389228   ENSP00000393350   ENSP00000403043  
     ENSP00000389080   ENSP00000385756   ENSP00000400214  

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    Cloud-Clone Corp. Proteins for TSSC1

     
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    antibodies-online proteins for TSSC1 (9 products) 

     
    antibodies-online peptides for TSSC1

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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:
    WDR: WD repeat domain containing

    4 InterPro protein domains:
     IPR019775 WD40_repeat_CS
     IPR001680 WD40_repeat
     IPR017986 WD40_repeat_dom
     IPR015943 WD40/YVTN_repeat-like_dom

    Graphical View of Domain Structure for InterPro Entry Q53HC9

    ProtoNet protein and cluster: Q53HC9

    UniProtKB/Swiss-Prot: TSSC1_HUMAN, Q53HC9
    Similarity: Contains 5 WD repeats


    Find genes that share domains with TSSC1           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:
         Genatlas biochemistry entry for TSSC1:
    tumor suppressing subchromosomal transferable DNA fragment (STF1),homolog of Rb associated protein p48 and
    Drosophila ,chromatin assembly factor 1 (CAF1),close to HBB@,not localized in the interval STIM1-NUP98

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with TSSC1           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for TSSC1

    miRNA
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    Inhib. RNA
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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
    cytoskeleton2
    cytosol1
    nucleus1

    (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 TSSC1
    Interactions:

        Search GeneGlobe Interaction Network for TSSC1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    Selected Interacting proteins for TSSC1 (Q53HC93 ENSP000003715594) via UniProtKB, MINT, STRING, and/or I2D (see all 9)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MOB1AQ9H8S93, ENSP000003793644I2D: score=2 STRING: ENSP00000379364
    CCAR2Q8N1633, ENSP000003106704I2D: score=1 STRING: ENSP00000310670
    CDK2P249413, ENSP000002669704I2D: score=1 STRING: ENSP00000266970
    SERBP1Q8NC513, ENSP000003600344I2D: score=1 STRING: ENSP00000360034
    TXNP105993, ENSP000003636414I2D: score=1 STRING: ENSP00000363641
    About this table

    (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 TSSC1



    (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 TSSC1 gene: 
    NM_003310.2  

    Unigene Cluster for TSSC1:

    Tumor suppressing subtransferable candidate 1
    Hs.502770  [show with all ESTs]
    Unigene Representative Sequence: AK126288
    14 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000478754(uc002qxi.2) ENST00000398659 ENST00000382125(uc002qxj.2)
    ENST00000496433 ENST00000455162 ENST00000441271 ENST00000463662 ENST00000482570
    ENST00000435721 ENST00000470625 ENST00000443925 ENST00000406835 ENST00000462515
    ENST00000444776
    miRNA
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    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat TSSC1
      QuantiFast Probe-based Assays in human, mouse, rat TSSC1

    Additional mRNA sequence: 

    AF019952.1 AK026522.1 AK126288.1 AK222652.1 BC002485.2 

    15 DOTS entries:

    DT.450242  DT.101983268  DT.100834396  DT.100834401  DT.75176254  DT.92441178  DT.97855520  DT.100834407 
    DT.120994072  DT.120994132  DT.40106649  DT.92441175  DT.95256812  DT.95358424  DT.95256840 

    Selected AceView cDNA sequences (see all 328):

    BI759730 BM474043 BU535460 BU944738 BI767735 BI765496 CR622340 AA447238 
    AA426440 BU164852 BM450805 BE047976 BM854924 BQ920851 CR621784 CR626366 
    BI823136 BQ216227 CR607271 BU176271 CR608131 AL555406 BI753239 BI761181 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for TSSC1 (see all 6)    About this scheme

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


    ECgene alternative splicing isoforms for TSSC1

    (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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    TSSC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTGTCCATCT
    TSSC1 Expression
    About this image


    TSSC1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Pancreas (Endocrine System)
             Islets of Langerhans
    TSSC1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TSSC1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.502770
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for TSSC1 gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tssc11 , 5 tumor suppressing subtransferable candidate 11, 5 87.05(n)1
    93.26(a)1
      12 (11.26 cM)5
    3807521  NM_201357.21  NP_958745.21 
     287518285 
    chicken
    (Gallus gallus)
    Aves TSSC11 tumor suppressing subtransferable candidate 1 83.27(n)
    92.67(a)
      421916  NM_001031088.1  NP_001026259.1 
    lizard
    (Anolis carolinensis)
    Reptilia TSSC16
    tumor suppressing subtransferable candidate 1
    91(a)
    1 ↔ 1
    1(162197223-162298722)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.61822 Xenopus laevis transcribed sequence with moderate similarity more 77.92(n)    BJ042010.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufj20b012 Transcribed sequence with moderate similarity to protein more 81.82(n)    CK360446.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG106461 , 3 CG106461 39(a)3
    50.62(n)1
    40.43(a)1
      69C43
    394261  NM_140324.31  NP_648581.11 
    worm
    (Caenorhabditis elegans)
    Secernentea Y87G2A.111 , 3 Y87G2A.111 34(a)3
    45.54(n)1
    37.18(a)1
      I(13597471-13606554)3
    1907781  NM_060982.41  NP_493383.11 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons DWA21 DWA2 47.09(n)
    38.25(a)
      843959  NM_106276.4  NP_177753.1 
    rice
    (Oryza sativa)
    Liliopsida Os08g05540001 Os08g0554000 47.06(n)
    39.71(a)
      4346273  NM_001068998.1  NP_001062463.1 


    ENSEMBL Gene Tree for TSSC1 (if available)
    TreeFam Gene Tree for TSSC1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TSSC1 gene
    1 SIMAP similar gene for TSSC1 using alignment to 8 protein entries:     TSSC1_HUMAN (see all proteins):
    WSB1

    Find genes that share paralogs with TSSC1           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 TSSC1 (see all 4835)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1411135331,2
    --3192266(+) AACCAC/TGAACA 1 -- int10--------
    rs1865453901,2
    --3192267(+) ACCACA/GAACAG 1 -- int10--------
    rs1502683111,2
    --3192418(+) CAGTGA/CGTGCG 1 -- int10--------
    rs1907210421,2
    --3192425(+) TGCGCA/GTGGGG 1 -- int10--------
    rs21679621,2
    C,F,A,H--3192427(-) CTCCCT/CACGCG 1 -- int116Minor allele frequency- C:0.46NS EA NA WA CSA 2260
    rs602942071,2
    --3192445(+) TGCCCA/GGCTCA 1 -- int10--------
    rs1832674961,2
    --3192481(+) ATGGGC/TTGCAG 1 -- int10--------
    rs1415475301,2
    C--3192521(+) CCTGCA/GTCTAC 1 -- int10--------
    rs1384042191,2
    C--3192623(+) GCGGCA/G/TTAGAC 1 -- int10--------
    rs1495839541,2
    --3192731(+) TGAGCA/CGAGCA 1 -- int10--------

    HapMap Linkage Disequilibrium report for TSSC1 (3192696 - 3381653 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for TSSC1 (see all 60):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2719491CNV Deletion23290073
    esv2535058CNV Deletion19546169
    esv2719498CNV Deletion23290073
    esv3034CNV Deletion18987735
    esv2719482CNV Deletion23290073
    dgv623e201CNV Deletion23290073
    esv1597731CNV Deletion17803354
    dgv622e201CNV Deletion23290073
    esv2719503CNV Deletion23290073
    esv2206412CNV Deletion18987734

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing TSSC1
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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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    OMIM gene information: 608998    OMIM disorders: --

    2 diseases for TSSC1:    
    About MalaCards
    wilms tumor    breast cancer


    Find genes that share disorders with TSSC1           About GenesLikeMe

    Genetic Association Database (GAD): TSSC1

    Export disorders for TSSC1 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 TSSC1 gene, integrated from 10 sources (see all 17):
    (articles sorted by number of sources associating them with TSSC1)
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    1. A 2.5-Mb transcript map of a tumor-suppressing subchromosomal transferable fragment from 11p15.5, and isolation and sequence analysis of three novel genes. (PubMed id 9403053)1, 2, 3 Hu R.-J.... Feinberg A.P. (Genomics 1997)
    2. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W.... Wilson R.K. (Nature 2005)
    3. 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)
    4. Subchromosomal assignment1 of the TSSC1 gene to human chromosome band 11p15.5 near the HBB gene cluster. (PubMed id 9925925)1, 3 Scelfo R....Negrini M. (Cytogenet. Cell Genet. 1998)
    5. Runx2 induces bone osteolysis by transcriptional suppression of TSSC1. (PubMed id 23933319)1 Wang D.C....Yuan Z.N. (Biochem. Biophys. Res. Commun. 2013)
    6. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (J. Cell. Sci. 2012)
    7. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    8. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    9. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    10. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 7260 HGNC: 12383 AceView: TSSC1 Ensembl:ENSG00000032389 euGenes: HUgn7260
    ECgene: TSSC1 H-InvDB: TSSC1

    (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 TSSC1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for TSSC1 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 TSSC1 gene:
    Search GeneIP for patents involving TSSC1

    GeneCards and IP:
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