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    SECTM1 secreted and transmembrane 1 [ Homo sapiens (human) ]

    Gene ID: 6398, updated on 11-Apr-2024

    Summary

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    Official Symbol
    SECTM1provided by HGNC
    Official Full Name
    secreted and transmembrane 1provided by HGNC
    Primary source
    HGNC:HGNC:10707
    See related
    Ensembl:ENSG00000141574 MIM:602602; AllianceGenome:HGNC:10707
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    K12; SECTM
    Summary
    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]
    Expression
    Broad expression in small intestine (RPKM 29.2), duodenum (RPKM 20.3) and 17 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SECTM1 in Genome Data Viewer
    Location:
    17q25.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (82321024..82333959, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (83189791..83202897, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (80278900..80291642, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12997 Neighboring gene long intergenic non-protein coding RNA 1970 Neighboring gene CSNK1D-CD7 intergenic CAGE-defined low expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80261261-80261761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80272095-80272682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9209 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80282821-80283426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80283427-80284032 Neighboring gene CD7 molecule Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80290146-80290948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80302606-80303141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13005 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:80309262-80309440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80309821-80310697 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80313765-80314700 Neighboring gene Sharpr-MPRA regulatory region 9771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80320818-80321596 Neighboring gene testis expressed 19 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80334527-80335396 Neighboring gene urotensin 2 receptor

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. The T/NK cell co-stimulatory molecule SECTM1 is an IFN "early response gene" that is negatively regulated by LPS in human monocytic cells. Huyton T, et al. Biochim Biophys Acta, 2011 Dec. PMID 21749909
    2. SECTM1 produced by tumor cells attracts human monocytes via CD7-mediated activation of the PI3K pathway. Wang T, et al. J Invest Dermatol, 2014 Apr. PMID 24157461, Free PMC Article
    3. Identification and characterization of K12 (SECTM1), a novel human gene that encodes a Golgi-associated protein with transmembrane and secreted isoforms. Slentz-Kesler KA, et al. Genomics, 1998 Feb 1. PMID 9480746
    4. 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. Bade-Döding C, et al. Biochim Biophys Acta, 2014 Mar. PMID 24211252
    5. Identification of CD7 as a cognate of the human K12 (SECTM1) protein. Lyman SD, et al. J Biol Chem, 2000 Feb 4. PMID 10652336

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CD7 is present on monocytes and tumor macrophages and its ligand, SECTM1, is frequently expressed in corresponding melanoma tissues
      Title: SECTM1 produced by tumor cells attracts human monocytes via CD7-mediated activation of the PI3K pathway.
    2. SECTM1 secreted from bone marrow stromal cells may interact with CD7 to influence GM-CSF expression in leukemic cells.
      Title: 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.
    3. level of SECTM1 expression is likely to be a key factor in innate immune responses and in the immune tolerance of cancerous cells
      Title: The T/NK cell co-stimulatory molecule SECTM1 is an IFN "early response gene" that is negatively regulated by LPS in human monocytic cells.
    4. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Polymorphisms in innate immunity genes and risk of childhood leukemia.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Risk of meningioma and common variation in genes related to innate immunity.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cytokine activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mesoderm development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of canonical NF-kappaB signal transduction HMP PubMed 
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in extracellular space TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    secreted and transmembrane protein 1
    Names
    type 1a transmembrane protein

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_003004.3 → NP_002995.1  secreted and transmembrane protein 1 precursor

      See identical proteins and their annotated locations for NP_002995.1

      Status: REVIEWED

      Source sequence(s)
      AC132872, BI861812, DA589733, U77643
      Consensus CDS
      CCDS11808.1
      UniProtKB/Swiss-Prot
      B2R7H0, O00466, Q8WVN6
      UniProtKB/TrEMBL
      A8K3U3, Q53G63
      Related
      ENSP00000269389.3, ENST00000269389.8
      Conserved Domains (1) summary
      pfam15492
      Location:6 → 152
      Nbas_N; Neuroblastoma-amplified sequence, N terminal

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      82321024..82333959 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005256392.4 → XP_005256449.1  secreted and transmembrane protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005256449.1

      UniProtKB/Swiss-Prot
      B2R7H0, O00466, Q8WVN6
      UniProtKB/TrEMBL
      A8K3U3, Q53G63
      Conserved Domains (1) summary
      pfam15492
      Location:6 → 152
      Nbas_N; Neuroblastoma-amplified sequence, N terminal

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      83189791..83202897 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316885.1 → XP_054172860.1  secreted and transmembrane protein 1 isoform X1

      UniProtKB/Swiss-Prot
      B2R7H0, O00466, Q8WVN6

    2. XM_054316886.1 → XP_054172861.1  secreted and transmembrane protein 1 isoform X1

      UniProtKB/Swiss-Prot
      B2R7H0, O00466, Q8WVN6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WVN6.2 GenPept UniProtKB/Swiss-Prot:Q8WVN6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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