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SECTM1 Gene

protein-coding   GIFtS: 53
GCID: GC17M080278

Secreted And Transmembrane 1

  See SECTM1-related disease
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
Secreted And Transmembrane 11 2
K122 3 5
Type 1a Transmembrane Protein1 2
K12 Protein1
Secreted And Transmembrane Protein 12
Protein K-123

External Ids:    HGNC: 107071   Entrez Gene: 63982   Ensembl: ENSG000001415747   OMIM: 6026025   UniProtKB: Q8WVN63   

Export aliases for SECTM1 gene to outside databases

Previous GC identifers: GC17P079165 GC17M083193 GC17M080808 GC17M080957 GC17M077872 GC17M075677


(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 SECTM1 Gene:
This gene encodes a transmembrane and secreted protein with characteristics of a type 1a transmembrane protein. It
is found in a perinuclear Golgi-like pattern and thought to be involved in hematopoietic and/or immune system
processes. (provided by RefSeq, Jul 2008)

GeneCards Summary for SECTM1 Gene:
SECTM1 (secreted and transmembrane 1) is a protein-coding gene. Diseases associated with SECTM1 include amblyopia. GO annotations related to this gene include cytokine activity and signal transducer activity.

UniProtKB/Swiss-Prot: SCTM1_HUMAN, Q8WVN6
Function: May be involved in thymocyte signaling

Gene Wiki entry for SECTM1 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_000017.10  NT_010663.16  NC_018928.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SECTM1 gene promoter:
         GCNF   HNF-4alpha2   HNF-4alpha1   MEF-2A   IRF-2   GCNF-1   IRF-7A   aMEF-2   GCNF-2   RSRFC4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSECTM1 promoter sequence
   Search Chromatin IP Primers for SECTM1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SECTM1


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

Entrez Gene cytogenetic band: 17q25   Ensembl cytogenetic band:  17q25.3   HGNC cytogenetic band: 17q25

SECTM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SECTM1 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M080278:  view genomic region     (about GC identifiers)

Start:
80,278,900 bp from pter      End:
80,291,950 bp from pter
Size:
13,051 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: SCTM1_HUMAN, Q8WVN6 (See protein sequence)
Recommended Name: Secreted and transmembrane protein 1 precursor  
Size: 248 amino acids; 27039 Da
Subunit: Interacts with CD7
Secondary accessions: B2R7H0 O00466

Explore the universe of human proteins at neXtProt for SECTM1: NX_Q8WVN6

Explore proteomics data for SECTM1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys181
  • Glycosylation2 at Asn56
  • Modification sites at PhosphoSitePlus

  • See SECTM1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_002995.1  
    ENSEMBL proteins: 
     ENSP00000269389   ENSP00000463904   ENSP00000464111   ENSP00000463114   ENSP00000463120  
     ENSP00000462563   ENSP00000462294   ENSP00000464385  

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    Sino Biological Recombinant Protein for SECTM1
    Sino Biological Cell Lysate for SECTM1
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    antibodies-online peptides for SECTM1

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    antibodies-online antibodies for SECTM1 (31 products) 

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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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    ProtoNet protein and cluster: Q8WVN6

    UniProtKB/Swiss-Prot: SCTM1_HUMAN, Q8WVN6
    Similarity: Belongs to the SECTM family


    (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:

         UniProtKB/Swiss-Prot Summary: SCTM1_HUMAN, Q8WVN6
    Function: May be involved in thymocyte signaling
    Induction: By IFNG/IFN-gamma (at protein level)

         Genatlas biochemistry entry for SECTM1:
    Golgi-associated protein,expressed in breast cancer cell lines and peripheral blood leucocyte,upstream of CD7

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004871signal transducer activity IMP12761501
    GO:0005125cytokine activity TAS9480746
         
    Find genes that share ontologies with SECTM1           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SECTM1

    miRNA
    Products:
        
    miRTarBase miRNAs that target SECTM1:
    hsa-mir-124-3p (MIRT022533)

    Block miRNA regulation of human, mouse, rat SECTM1 using miScript Target Protectors
    Search for qRT-PCR Assays for microRNAs that regulate SECTM1
    SwitchGear 3'UTR luciferase reporter plasmidSECTM1 3' UTR sequence
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    Predesigned siRNA for gene silencing in human, mouse, rat SECTM1

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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
    SCTM1_HUMAN, Q8WVN6: Cell membrane; Single-pass type I membrane protein (Probable). Secreted
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    plasma membrane5
    golgi apparatus4

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space TAS9480746
    GO:0005794Golgi apparatus TAS9480746
    GO:0005886plasma membrane IEA--
    GO:0016021integral component of membrane IEA--
    GO:0070062extracellular vesicular exosome IDA19056867

    Find genes that share ontologies with SECTM1           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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    SuperPaths for SECTM1 About    
    See pathways by source

    SuperPathContained pathways About
    1TNF Signaling
    NF-kB (NFkB) Pathway0.46


    1 Sino Biological Pathway for SECTM1
        NF-kB (NFkB) Pathway


        Pathway & Disease-focused RT2 Profiler PCR Array including SECTM1: 
              Inflammatory Response & Autoimmunity 384HT in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for SECTM1

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for SECTM1 (Q8WVN63 ENSP000002693894) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CD7P095643, ENSP000003120274I2D: score=3 STRING: ENSP00000312027
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006955immune response TAS9480746
    GO:0007165signal transduction IMP12761501
    GO:0007498mesoderm development TAS9480746
    GO:0043123positive regulation of I-kappaB kinase/NF-kappaB signaling IMP12761501

    Find genes that share ontologies with SECTM1           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 SECTM1 (SCTM1)



    (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 SECTM1 gene: 
    NM_003004.2  

    Unigene Cluster for SECTM1:

    Secreted and transmembrane 1
    Hs.558009  [show with all ESTs]
    Unigene Representative Sequence: NM_003004
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000269389(uc002keo.3) ENST00000580437 ENST00000581864 ENST00000581691
    ENST00000582563 ENST00000583093 ENST00000582290 ENST00000581954
    miRNA
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    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat SECTM1
      QuantiFast Probe-based Assays in human, mouse, rat SECTM1

    Additional mRNA sequence: 

    AK223068.1 AK223104.1 AK290708.1 AK312980.1 BC017716.1 U77643.1 

    7 DOTS entries:

    DT.403344  DT.120937834  DT.100720762  DT.100806701  DT.100806712  DT.100806710  DT.95113527 

    Selected AceView cDNA sequences (see all 130):

    BI761265 CR614987 CR620624 CR625551 AW057702 CF140805 CR594943 AW002382 
    BQ946621 BM755524 AA826896 BM053069 BU689727 BF939675 CR594118 BX396113 
    CK903980 BX399171 CR606594 CR591775 CD364677 BF002304 BX417901 CR595956 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SECTM1 (see all 11)    About this scheme

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


    ECgene alternative splicing isoforms for SECTM1

    (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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    SECTM1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACTCGAATAT
    SECTM1 Expression
    About this image

    SECTM1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SECTM1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.558009

    UniProtKB/Swiss-Prot: SCTM1_HUMAN, Q8WVN6
    Tissue specificity: Detected at the highest levels in peripheral blood leukocytes and breast cancer cell lines.
    Found in leukocytes of the myeloid lineage, with the strongest expression observed in granulocytes and no
    detectable expression in lymphocytes. Expressed in thymic epithelial cells and fibroblasts

        Pathway & Disease-focused RT2 Profiler PCR Array including SECTM1: 
              Inflammatory Response & Autoimmunity 384HT in human mouse rat

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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 human and mouse.

    Orthologs for SECTM1 gene from Selected species (see all 4)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sectm1a1 , 5 secreted and transmembrane 1A1, 5 65.13(n)1
    47.98(a)1
      11 (84.89 cM)5
    2095881  NM_145373.21  NP_663348.21 
     1210674075 


    ENSEMBL Gene Tree for SECTM1 (if available)
    TreeFam Gene Tree for SECTM1 (if available)

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

    (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 SECTM1 (see all 363)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1445911491,2
    --80278494(+) AACAGA/TAGCAG 1 -- ds50010--------
    rs2014703201,2
    C--80278783(-) CTTTTC/TTCTTT 1 -- ds50010--------
    rs1155431771,2
    F--80278862(+) ACCCCC/TGTGCG 1 -- ds50011Minor allele frequency- T:0.03WA 118
    rs115750341,2
    C,F--80278867(-) ACCCCC/TGCACG 1 -- ds50015Minor allele frequency- T:0.41NA EA 284
    rs115750331,2
    C,F,H--80278956(-) TCCAAG/AAGGGG 1 -- ut31 ese38Minor allele frequency- A:0.14NA NS CSA WA 950
    rs1869406131,2
    --80278972(+) GCTCCA/GGCCCG 1 -- ut310--------
    rs1133450331,2
    C,F--80279007(+) AGGCCC/TCGGTC 1 -- ut311Minor allele frequency- T:0.50NA 2
    rs1401868391,2
    --80279036(+) CCTGCC/GGGGTC 1 -- ut310--------
    rs1502469231,2
    C--80279158(+) AAATTC/GCATTT 1 -- ut310--------
    rs1830832781,2
    --80279289(+) GACATC/TAAAGG 1 -- ut310--------

    HapMap Linkage Disequilibrium report for SECTM1 (80278900 - 80291950 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SECTM1 (see all 20):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1009380CNV Insertion20482838
    nsv909223CNV Loss21882294
    nsv909220CNV Loss21882294
    dgv3354n71CNV Loss21882294
    dgv3357n71CNV Loss21882294
    dgv3353n71CNV Loss21882294
    nsv909134CNV Loss21882294
    dgv3356n71CNV Loss21882294
    dgv3341n71CNV Loss21882294
    dgv3332n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SECTM1
    DNA2.0 Custom Variant and Variant Library Synthesis for SECTM1

    (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: 602602    OMIM disorders: --

    1 disease for SECTM1:    
    About MalaCards
    amblyopia

    2 diseases from the University of Copenhagen DISEASES database for SECTM1:
    Corneal dystrophy     Amblyopia

    Find genes that share disorders with SECTM1           About GenesLikeMe

    Genetic Association Database (GAD): SECTM1
    Human Genome Epidemiology (HuGE) Navigator: SECTM1 (4 documents)

    Export disorders for SECTM1 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 SECTM1 gene, integrated from 10 sources (see all 20):
    (articles sorted by number of sources associating them with SECTM1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of K12 (SECTM1), a novel human gene that encodes a Golgi-associated protein with transmembrane and secreted isoforms. (PubMed id 9480746)1, 2, 3, 9 Slentz-Kesler K.A.... Kaufman R.E. (Genomics 1998)
    2. Identification of CD7 as a cognate of the human K12 (SECTM1) protein. (PubMed id 10652336)1, 2, 9 Lyman S.D.... Fanslow W.C. (J. Biol. Chem. 2000)
    3. Polymorphisms in innate immunity genes and risk of childhood leukemia. (PubMed id 20438785)1, 4 Han S....Kang D. (Hum. Immunol. 2010)
    4. Risk of meningioma and common variation in genes related to innate immunity. (PubMed id 20406964)1, 4 Rajaraman P....Inskip P.D. (amp 2010)
    5. 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)
    6. Expression of the CD7 ligand K-12 in human thymic epithelial cells: regulation by IFN-gamma. (PubMed id 15742156)2, 9 Lam G.K.... Haynes B.F. (J. Clin. Immunol. 2005)
    7. Autocrine GM-CSF transcription in the leukemic progenitor cell line KG1a is mediated by the transcription factor ETS1 and is negatively regulated through SECTM1 mediated ligation of CD7. (PubMed id 24211252)1 Bade-DAPding C....Huyton T. (Biochim. Biophys. Acta 2014)
    8. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    9. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    10. The T/NK cell co-stimulatory molecule SECTM1 is an IFN &quot;early response gene&quot; that is negatively regulated by LPS in human monocytic cells. (PubMed id 21749909)1 Huyton T....Blasczyk R. (Biochim. Biophys. Acta 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: 6398 HGNC: 10707 AceView: SECTM1 Ensembl:ENSG00000141574 euGenes: HUgn6398
    ECgene: SECTM1 H-InvDB: SECTM1

    (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 SECTM1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for SECTM1 gene:
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