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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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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

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