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THSD1 Gene

protein-coding   GIFtS: 52
GCID: GC13M052935

Thrombospondin, Type I, Domain Containing 1

(Previous names: thrombospondin, type I, domain 1)
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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
Thrombospondin, Type I, Domain Containing 11 2     4833423O18Rik2
Thrombospondin, Type I, Domain 11 2     UNQ30102
Transmembrane Molecule With Thrombospondin Module2 3     Thrombospondin Type-1 Domain-Containing Protein 12
TMTSP2 3     

External Ids:    HGNC: 177541   Entrez Gene: 559012   Ensembl: ENSG000001361147   UniProtKB: Q9NS623   

Export aliases for THSD1 gene to outside databases

Previous GC identifers: GC13M046946 GC13M051887 GC13M050749 GC13M051849 GC13M033689


(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 THSD1 Gene:
The protein encoded by this gene contains a type 1 thrombospondin domain, which is found in a number of proteins
involved in the complement pathway, as well as in extracellular matrix proteins. Alternatively spliced transcript
variants encoding different isoforms have been observed for this gene. (provided by RefSeq, Jan 2009)

GeneCards Summary for THSD1 Gene:
THSD1 (thrombospondin, type I, domain containing 1) is a protein-coding gene.

Gene Wiki entry for THSD1 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_000013.10  NC_018924.2  NT_024524.15  
Regulatory elements:
   Regulatory transcription factor binding sites in the THSD1 gene promoter:
         NF-AT4   NF-AT2   AP-1   POU2F1   FOXJ2 (long isoform)   POU2F1a   NF-AT3   FOXJ2   NF-AT1   NF-AT   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTHSD1 promoter sequence
   Search Chromatin IP Primers for THSD1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat THSD1


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

Entrez Gene cytogenetic band: 13q14.3   Ensembl cytogenetic band:  13q14.3   HGNC cytogenetic band: 13q14.13

THSD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
THSD1 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M052935:  view genomic region     (about GC identifiers)

Start:
52,951,302 bp from pter      End:
52,980,629 bp from pter
Size:
29,328 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: THSD1_HUMAN, Q9NS62 (See protein sequence)
Recommended Name: Thrombospondin type-1 domain-containing protein 1 precursor  
Size: 852 amino acids; 94584 Da
Secondary accessions: A2A3J3 B2RCF5 Q6P3U1 Q6UXZ2
Alternative splicing: 3 isoforms:  Q9NS62-1   Q9NS62-2   Q9NS62-3   

Explore the universe of human proteins at neXtProt for THSD1: NX_Q9NS62

Explore proteomics data for THSD1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn39, Asn53, Asn58, Asn69, Asn80, Asn135, Asn304
  • Modification sites at PhosphoSitePlus

  • See THSD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_061146.1  NP_954872.1  

    ENSEMBL proteins: 
     ENSP00000340650   ENSP00000258613   ENSP00000438512  
    Reactome Protein details: Q9NS62

    THSD1 Human Recombinant Protein Products:

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    antibodies-online proteins for THSD1 (11 products) 

     
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    antibodies-online kits for THSD1 (6 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR000884 Thrombospondin_1_rpt

    Graphical View of Domain Structure for InterPro Entry Q9NS62

    ProtoNet protein and cluster: Q9NS62

    1 Blocks protein domain: IPB008085 Thrombospondin type 1 repeat signature

    UniProtKB/Swiss-Prot: THSD1_HUMAN, Q9NS62
    Similarity: Contains 1 TSP type-1 domain


    Find genes that share domains with THSD1           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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    Phenotypes:
         1 GenomeRNAi human phenotype for THSD1:
     Large nuclei 

         1 MGI mutant phenotype (inferred from 2 alleles(MGI details for Thsd1):
     no phenotypic analysis 

    Find genes that share phenotypes with THSD1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Thsd1tm1(KOMP)Vlcg for THSD1

       genOway: Develop your customized and physiologically relevant rodent model for THSD1

    miRNA
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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
    THSD1_HUMAN, Q9NS62: Isoform 1: Membrane; Single-pass type I membrane protein (Potential)
    THSD1_HUMAN, Q9NS62: Isoform 2: Membrane; Single-pass type I membrane protein (Potential)
    THSD1_HUMAN, Q9NS62: Isoform 3: Secreted
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    cytosol4
    plasma membrane3
    endoplasmic reticulum1
    mitochondrion1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--
    GO:0005737cytoplasm IDA--
    GO:0009986cell surface IEA--
    GO:0016021integral component of membrane IEA--
    GO:0071944cell periphery IEA--

    Find genes that share ontologies with THSD1           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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    Find genes that share SuperPaths with THSD1           About GenesLikeMe

    Pathways by sourceSee SuperPaths
    Show all pathways



    1 Reactome Pathway for THSD1
        O-glycosylation of TSR domain-containing proteins


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for THSD1
    Interactions:

        Search GeneGlobe Interaction Network for THSD1

    1 Interacting protein for THSD1 (Q9NS623) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TLN1Q9Y4903I2D: score=1 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002244hematopoietic progenitor cell differentiation IEA--

    Find genes that share ontologies with THSD1           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 THSD1



    (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 THSD1 gene (2 alternative transcripts): 
    NM_018676.3  NM_199263.2  

    Unigene Cluster for THSD1:

    Thrombospondin, type I, domain containing 1
    Hs.325667  [show with all ESTs]
    Unigene Representative Sequence: NM_018676
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000349258(uc001vgo.3 uc001vgp.3 uc010tgz.2) ENST00000258613
    ENST00000544466
    miRNA
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    Additional mRNA sequence: 

    AB044385.1 AK096289.1 AK298974.1 AK315087.1 AY358149.1 BC063842.1 

    5 DOTS entries:

    DT.100742202  DT.86853979  DT.99928044  DT.120790671  DT.91897683 

    Selected AceView cDNA sequences (see all 314):

    BC037279 CA944508 BG982544 BQ029526 H58321 AW592631 AI554215 BE855758 
    AI161038 BM972213 BU074192 CR590821 AI208829 BM711180 AA844672 CK818951 
    CR616305 AI683536 CK820208 BX107214 AI565139 AA516386 BM977930 AA905651 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for THSD1    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b
    SP1:                                    
    SP2:        -     -     -               


    ECgene alternative splicing isoforms for THSD1

    (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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    THSD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTTTGAATT
    THSD1 Expression
    About this image


    THSD1 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
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 2 entries
             Muscle Progenitor Cells Mandibular Arch Muscles
     
     Liver (Hepatobiliary System)
             Hematopoietic Stem Cells Liver Bud
     
     Blood (Cardiovascular System)
             Hematopoietic Stem Cells Liver Bud
     
     Neural Tube (Nervous System)
             Telencephalon
    THSD1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    THSD1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.325667
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for THSD1

    (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 THSD1 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Thsd11 , 5 thrombospondin, type I, domain 11, 5 80.53(n)1
    78.73(a)1
      8 (11.16 cM)5
    562291  NM_019576.21  NP_062522.11 
     222273135 
    chicken
    (Gallus gallus)
    Aves THSD11 thrombospondin, type I, domain containing 1 65.71(n)
    60.22(a)
      418884  XM_417078.3  XP_417078.1 
    lizard
    (Anolis carolinensis)
    Reptilia THSD16
    thrombospondin, type I, domain containing 1
    49(a)
    1 ↔ 1
    1(132655897-132672863)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia thsd11 thrombospondin, type I, domain containing 1 56.13(n)
    48.08(a)
      100497491  XM_004911971.1  XP_004912028.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC7975201 thrombospondin type-1 domain-containing protein 1-like 49.92(n)
    39.97(a)
      797520  XM_001337954.4  XP_001337990.3 


    ENSEMBL Gene Tree for THSD1 (if available)
    TreeFam Gene Tree for THSD1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for THSD1 gene

    Find genes that share paralogs with THSD1           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for THSD1
    PGOHUM00000248403


    (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 THSD1 (see all 678)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs612858381,2
    C,F--52950929(+) ACATTA/CTCTCT 2 -- ds50012Minor allele frequency- C:0.04WA 120
    rs600453801,2
    C,F--52950960(+) ATAATT/CTTGTC 2 -- ds50011Minor allele frequency- C:0.04WA 118
    rs1178202201,2
    C,F--52950987(+) ACTCTA/CATCTG 2 -- ds50011Minor allele frequency- C:0.03NA 120
    rs1916547261,2
    --52950990(+) CTAATC/GTGAAA 2 -- ds50010--------
    rs1389720631,2
    --52951246(+) AGCATA/GTTCTA 2 -- ds50010--------
    rs1143494261,2
    C,F--52951269(+) ATCTTA/GTCTTT 2 -- ds50011Minor allele frequency- G:0.03WA 118
    rs79973891,2
    C--52951302(+) CCCCAC/TTTGCT 2 -- ut310--------
    rs95360411,2,,4
    C,F,H--52951802(+) CACTCT/CTGTGA 4 /K /R mis1 ese317Minor allele frequency- C:0.04NS EA NA EU 7898
    rs2002932271,2
    --52951826(+) CCCGAC/TGAGCT 4 H R mis10--------
    rs1844749671,2
    C--52951881(+) GTGATC/GCCCAA 4 H D mis10--------

    HapMap Linkage Disequilibrium report for THSD1 (52951302 - 52980629 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for THSD1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv994275CNV Loss20482838
    nsv428288CNV Loss18775914
    nsv900084CNV Gain21882294
    nsv7242OTHER Inversion18451855

    Site Specific Mutation Identification with PCR Assays
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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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    Find genes that share disorders with THSD1           About GenesLikeMe

    Genetic Association Database (GAD): THSD1

    Export disorders for THSD1 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 THSD1 gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with THSD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)1, 2 Dunham A.... Ross M.T. (Nature 2004)
    2. 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)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    5. Monochromosome transfer and microarray analysis identify a critical tumor-suppressive region mapping to chromosome 13q14 and THSD1 in esophageal carcinoma. (PubMed id 18403638)1, 9 Ko J.M....Lung M.L. (Mol. Cancer Res. 2008)
    6. Genome-wide screening for methylation-silenced genes in colorectal cancer. (PubMed id 22664866)1 Khamas A....Sugihara K. (Int. J. Oncol. 2012)
    7. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    8. Immunolocalization of thrombospondin in the human and sand rat intervertebral disc. (PubMed id 17047544)1 Gruber H.E....Hanley E.N. (Spine 2006)
    9. Thrombospondin induces RhoA inactivation through FAK-dependent signaling to stimulate focal adhesion disassembly. (PubMed id 15371459)1 Orr A.W....Murphy-Ullrich J.E. (J. Biol. Chem. 2004)
    10. 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: 55901 HGNC: 17754 AceView: C13orf9andTHSD1 Ensembl:ENSG00000136114 euGenes: HUgn55901
    ECgene: THSD1 H-InvDB: THSD1

    (According to HUGE)
    About This Section

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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)
    About This Section

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    NameDescription
    PharmGKB entry for THSD1 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 THSD1 gene:
    Search GeneIP for patents involving THSD1

    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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