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TM9SF1 Gene

protein-coding   GIFtS: 50
GCID: GC14M024658

Transmembrane 9 Superfamily Member 1

  See 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
Transmembrane 9 Superfamily Member 11 2     Multispanning Membrane Protein (70kD)2
MP70 Protein Family Member2 3     Transmembrane Protein 9 Superfamily Member 12
HMP702     hMP703
MP702     

External Ids:    HGNC: 118641   Entrez Gene: 105482   Ensembl: ENSG000001009267   UniProtKB: O153213   

Export aliases for TM9SF1 gene to outside databases

Previous GC identifers: GC14M022030 GC14M018445 GC14M022648 GC14M023728 GC14M004773


(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 TM9SF1 Gene:
TM9SF1 (transmembrane 9 superfamily member 1) is a protein-coding gene. Diseases associated with TM9SF1 include prostate cancer, and prostatitis. An important paralog of this gene is TM9SF3.

UniProtKB/Swiss-Prot: TM9S1_HUMAN, O15321
Function: Plays an essential role in autophagy




(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:
NC_000014.9  NC_018925.2  NT_026437.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the TM9SF1 gene promoter:
         RFX1   Lmo2   RelA   Nkx2-5   Nkx5-1   c-Ets-1   GATA-1   PPAR-gamma1   PPAR-gamma2   NF-E2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTM9SF1 promoter sequence
   Search Chromatin IP Primers for TM9SF1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TM9SF1


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

Entrez Gene cytogenetic band: 14q11.2   Ensembl cytogenetic band:  14q12   HGNC cytogenetic band: 14q11.2

TM9SF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TM9SF1 gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14M024658:  view genomic region     (about GC identifiers)

Start:
24,658,349 bp from pter      End:
24,682,679 bp from pter
Size:
24,331 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TM9S1_HUMAN, O15321 (See protein sequence)
Recommended Name: Transmembrane 9 superfamily member 1 precursor  
Size: 606 amino acids; 68861 Da
Secondary accessions: D3DS65 Q86SZ6 Q96FI8
Alternative splicing: 2 isoforms:  O15321-1   O15321-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TM9SF1: NX_O15321

Explore proteomics data for TM9SF1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn178, Asn401, Asn559
  • Modification sites at PhosphoSitePlus

  • See TM9SF1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001014842.1  NP_001275935.1  NP_006396.2  

    ENSEMBL proteins: 
     ENSP00000261789   ENSP00000432997   ENSP00000431747   ENSP00000434387   ENSP00000436486  
     ENSP00000380063   ENSP00000431447   ENSP00000437127   ENSP00000435857   ENSP00000432435  
     ENSP00000433792   ENSP00000451949  

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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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    1 InterPro protein domain:
     IPR004240 EMP70

    Graphical View of Domain Structure for InterPro Entry O15321

    ProtoNet protein and cluster: O15321

    1 Blocks protein domain: IPB004240 Nonaspanin (TM9SF)

    UniProtKB/Swiss-Prot: TM9S1_HUMAN, O15321
    Similarity: Belongs to the nonaspanin (TM9SF) family


    TM9SF1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TM9S1_HUMAN, O15321
    Function: Plays an essential role in autophagy

         Genatlas biochemistry entry for TM9SF1:
    transmembrane 9 superfamily,member 1,ubiquitously expressed

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TM9SF1
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    miRNA
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    miRTarBase miRNAs that target TM9SF1:
    hsa-mir-615-3p (MIRT040194), hsa-mir-107 (MIRT048305), hsa-mir-30a-5p (MIRT028483)

    Block miRNA regulation of human, mouse, rat TM9SF1 using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate TM9SF1:
    hsa-miR-3671 hsa-miR-590-3p
    SwitchGear 3'UTR luciferase reporter plasmidTM9SF1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat TM9SF1

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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
    TM9S1_HUMAN, O15321: Lysosome membrane; Multi-pass membrane protein. Cytoplasmic vesicle, autophagosome membrane;
    Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    lysosome5
    vacuole5
    plasma membrane3
    endoplasmic reticulum1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000421autophagic vacuole membrane IEA--
    GO:0005765lysosomal membrane IEA--
    GO:0016021integral component of membrane IEA--
    GO:0031410cytoplasmic vesicle IEA--

    TM9SF1 for ontologies           About GeneDecksing


    (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 TM9SF1
    Interactions:

        Search GeneGlobe Interaction Network for TM9SF1

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

    Selected Interacting proteins for TM9SF1 (O153213 ENSP000002617894) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MMEP084733I2D: score=2 
    CLN3Q132863I2D: score=1 
    ATP6V1AENSP000002733984STRING: ENSP00000273398
    P2RX7ENSP000002618264STRING: ENSP00000261826
    RNASEH1ENSP000003133504STRING: ENSP00000313350
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    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006914autophagy IEA--
    GO:0015031protein transport ----

    TM9SF1 for ontologies           About GeneDecksing



    (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 TM9SF1 (TM9S1)



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for TM9SF1 gene (3 alternative transcripts): 
    NM_001014842.2  NM_001289006.1  NM_006405.6  

    Unigene Cluster for TM9SF1:

    Transmembrane 9 superfamily member 1
    Hs.91586  [show with all ESTs]
    Unigene Representative Sequence: NM_006405
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000261789(uc010toa.1 uc001wnb.1) ENST00000528669 ENST00000529332
    ENST00000524835 ENST00000532632 ENST00000396854(uc001wnc.3) ENST00000531406
    ENST00000528895 ENST00000530563 ENST00000530468 ENST00000525592 ENST00000528010
    ENST00000556387
    miRNA
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    2 qRT-PCR Assays for microRNAs that regulate TM9SF1:
    hsa-miR-3671 hsa-miR-590-3p
    SwitchGear 3'UTR luciferase reporter plasmidTM9SF1 3' UTR sequence
    Inhib. RNA
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat TM9SF1
      QuantiTect SYBR Green Assays in human, mouse, rat TM9SF1
      QuantiFast Probe-based Assays in human, mouse, rat TM9SF1

    Additional mRNA sequence: 

    AK292110.1 AK304642.1 BC010856.2 BX161390.1 BX161494.1 U94831.1 

    20 DOTS entries:

    DT.316366  DT.100858196  DT.100858198  DT.101984522  DT.100858200  DT.100858188  DT.316365  DT.100723743 
    DT.95190065  DT.120755398  DT.95094529  DT.100770753  DT.316368  DT.99951905  DT.100858189  DT.100772236 
    DT.100858191  DT.95210591  DT.99999972  DT.86997836 

    Selected AceView cDNA sequences (see all 647):

    BX161494 CR618221 BX332624 BE549758 AA427665 AW205944 BQ070636 AI638805 
    AI391505 AI420371 BM453288 BX367924 CN484799 BU186741 BU158214 AA436865 
    BX374395 BQ431862 CB241575 NM_024658 BU527086 BE909061 BQ962842 BU624905 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for TM9SF1 (see all 10)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b · 10c
    SP1:                                                                                            -           -     -                                       
    SP2:                                -                 -     -     -     -     -     -     -     -     -     -     -     -     -                           
    SP3:                                                                                            -           -     -                                       
    SP4:                    -     -     -     -                                                                                                               
    SP5:                                -     -                                                                                                               


    ECgene alternative splicing isoforms for TM9SF1

    (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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    TM9SF1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCCTGTTGAA
    TM9SF1 Expression
    About this image

    TM9SF1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TM9SF1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.91586

    UniProtKB/Swiss-Prot: TM9S1_HUMAN, O15321
    Tissue specificity: Expressed in lung, pancreas, kidney, liver, placenta, skeletal muscle, heart and brain. The
    amount in skeletal muscle, heart and brain were considerably lower than in the other tissues

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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 TM9SF1 gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tm9sf11 , 5 transmembrane 9 superfamily member 11, 5 92.96(n)1
    97.52(a)1
      14 (28.19 cM)5
    741401  NM_028780.31  NP_083056.21 
     556359655 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    87(a)
    1 → many
    GL343400.1(53222-64987)
    African clawed frog
    (Xenopus laevis)
    Amphibia 480506642   -- 77.03(n)    48050664 
    zebrafish
    (Danio rerio)
    Actinopterygii tm9sf11 transmembrane 9 superfamily member 1 70.49(n)
    76.01(a)
      445156  NM_001003550.2  NP_001003550.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes EMP706
    TMN26
    Protein with a role in cellular adhesion, filament...
    Protein with a role in cellular adhesion and filam...
    27(a)
    26(a)
    many ↔ many
    many ↔ many
    XII(294091-296094) YLR083C
    IV(669016-671034) YDR107C
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G019701 AT2G01970 53.8(n)
    49.29(a)
      814728  NM_126258.2  NP_178306.1 
    rice
    (Oryza sativa)
    Liliopsida Os.473652 Oryza sativa (japonica cultivar-group) putative Transmembrane more 80.58(n)    NM_189098.1 


    ENSEMBL Gene Tree for TM9SF1 (if available)
    TreeFam Gene Tree for TM9SF1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TM9SF1 gene
    TM9SF32  ENSG000002546922  ENSG000002595222  TM9SF22  TM9SF42  
    9 SIMAP similar genes for TM9SF1 using alignment to 11 protein entries:     TM9S1_HUMAN (see all proteins):
    CHMP4A    CHMP4B    CHMP4BP1    CHMP4C    SMBP    TM9SF3
    CHMP6    TM9SF4    TM9SF2

    TM9SF1 for paralogs           About GeneDecksing



    (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 TM9SF1 (see all 174)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 14 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs286368041,2
    C--24660216(+) ACAGGC/TGCCCG 2 -- int10--------
    rs37425031,2
    C,F--24660228(+) CACCAT/CGCCCG 2 -- int15Minor allele frequency- C:0.44NA WA CSA 9
    rs37425041,2
    C,F,A--24660323(+) GCCTCG/AGCCTC 2 -- int14Minor allele frequency- A:0.29NA WA CSA 7
    rs1498123671,2
    --24660361(+) CCACCA/GCACCC 2 -- int10--------
    rs10618381,2
    C,F,A,H--24660406(-) ACCGGG/CTTGGG 2 -- int117Minor allele frequency- C:0.47NS EA NA WA CSA 1167
    rs726943041,2
    C--24660498(+) AGTTGG/TTAATT 2 -- int13Minor allele frequency- T:0.22CSA NA EA 242
    rs1447904691,2
    --24660570(+) AAATGG/TGATGG 2 -- int10--------
    rs1401348931,2
    --24660647(+) AAAGGA/GCAATC 2 -- int10--------
    rs1846607061,2
    --24660746(+) GCTGAA/GACCTA 2 -- int10--------
    rs1454285981,2
    --24660802(+) AGCCTG/TTAGTT 2 -- int10--------

    HapMap Linkage Disequilibrium report for TM9SF1 (24658349 - 24682679 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for TM9SF1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv1220CNV Insertion18451855
    nsv901498CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing TM9SF1
    DNA2.0 Custom Variant and Variant Library Synthesis for TM9SF1

    (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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    2 diseases for TM9SF1:    
    About MalaCards
    prostate cancer    prostatitis


    TM9SF1 for disorders           About GeneDecksing


    Export disorders for TM9SF1 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 TM9SF1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with TM9SF1)
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    1. Cloning of a human multispanning membrane protein cDNA: evidence for a new protein family. (PubMed id 9332367)1, 2, 3, 9 Chluba-de Tapia J.... Eberle A.N. (Gene 1997)
    2. High-throughput functional screening for autophagy-related genes and identification of TM9SF1 as an autophagosome-inducing gene. (PubMed id 19029833)1, 2 He P.... Ma D. (Autophagy 2009)
    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. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
    5. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    6. ErbB2-associated changes in the lysosomal proteome. (PubMed id 21674799)1 Nylandsted J....JAoAottelAo M. (Proteomics 2011)
    7. HSP27 and HSP70 interact with CD10 in C4-2 prostate cancer cells. (PubMed id 17342744)1 Dall'Era M.A....Liu A.Y. (Prostate 2007)
    8. The DNA sequence and analysis of human chromosome 14. (PubMed id 12508121)2 Heilig R.... Weissenbach J. (Nature 2003)
    9. 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)
    10. The iodocyanopindolol and SM-11044 binding protein belongs to the TM9SF multispanning membrane protein superfamily. (PubMed id 11595169)1 Sugasawa T....Nahmias C. (Gene 2001)

    (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: 10548 HGNC: 11864 AceView: TM9SF1andIPO4 Ensembl:ENSG00000100926 euGenes: HUgn10548
    ECgene: TM9SF1 H-InvDB: TM9SF1

    (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 TM9SF1 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 TM9SF1 gene:
    Search GeneIP for patents involving TM9SF1

    GeneCards and IP:
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