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    SMIM10L2A small integral membrane protein 10 like 2A [ Homo sapiens (human) ]

    Gene ID: 399668, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SMIM10L2Aprovided by HGNC
    Official Full Name
    small integral membrane protein 10 like 2Aprovided by HGNC
    Primary source
    HGNC:HGNC:34499
    See related
    Ensembl:ENSG00000178947 AllianceGenome:HGNC:34499
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LED; LINC0086; LINC00086; LINC00087; SMIM10L2B; NCRNA00086; NCRNA00087
    Summary
    This gene encodes a highly conserved small protein that contains a conserved motif (DUF4560) and may function as an integral membrane protein. This transcript was also shown to associate with enhancer chromatin and therefore may also function as an RNA to regulate enhancers. [provided by RefSeq, Jan 2017]
    Expression
    Biased expression in adrenal (RPKM 10.3), brain (RPKM 9.2) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMIM10L2A in Genome Data Viewer
    Location:
    Xq26.3
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (135421944..135428075)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (133747687..133753818)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (134555869..134562000)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21019 Neighboring gene zinc finger protein 449 Neighboring gene uncharacterized LOC100506790 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:134539161-134540038 Neighboring gene NANOG hESC enhancer GRCh37_chrX:134542673-134543175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21020 Neighboring gene RNA, 5S ribosomal pseudogene 515 Neighboring gene CROCC pseudogene 1

    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. Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA. Léveillé N, et al. Nat Commun, 2015 Mar 27. PMID 25813522, Free PMC Article
    2. Potential diagnostic and prognostic value of plasma long noncoding RNA LINC00086 and miR-214 expression in gastric cancer. Ji B, et al. Cancer Biomark, 2019. PMID 30689553
    3. Long Noncoding RNA LINC0086 Functions as a Tumor Suppressor in Nasopharyngeal Carcinoma by Targeting miR-214. Guo J, et al. Oncol Res, 2017 Aug 7. PMID 28245169, Free PMC Article
    4. Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: over 6000 non-redundant transcripts, novel genes and splice variants. Wistow G, et al. Mol Vis, 2002 Jun 15. PMID 12107410
    5. The DNA sequence of the human X chromosome. Ross MT, et al. Nature, 2005 Mar 17. PMID 15772651, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Plasma long noncoding RNA LINC00086 expression is significantly lower in gastric cancer (GC) patients than in normal individuals. GC patients with low LINC00086 expression are likely to have larger tumors, lymphatic metastasis, larger TNM stage, and higher carcinoembryonic antigen and carbohydrate antigen 19-9 levels. GC patients with low LINC00086 expression show lower survival rates.
      Title: Potential diagnostic and prognostic value of plasma long noncoding RNA LINC00086 and miR-214 expression in gastric cancer.
    2. tumor-suppressive role of LINC0086 in NPC. Low expression of LINC0086 is associated with a poor prognosis of NPC patients. Upregulation of LINC0086 significantly inhibited NPC cancer cell growth and caused apoptosis in vitro and in vivo by targeting miR-214.
      Title: Long Noncoding RNA LINC0086 Functions as a Tumor Suppressor in Nasopharyngeal Carcinoma by Targeting miR-214.
    Submit: New GeneRIF Correction

    Phenotypes

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    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • MGC39606

    General protein information

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    Preferred Names
    small integral membrane protein 10-like protein 2A
    Names
    Small integral membrane protein 10-like protein 2B
    lncRNA activator of enhancer domains
    long intergenic non-protein coding RNA 86

    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_203306.3 → NP_976051.1  small integral membrane protein 10-like protein 2A

      Status: VALIDATED

      Source sequence(s)
      AL450472
      UniProtKB/Swiss-Prot
      P0DMW4, P0DMW5
      Related
      ENSP00000488643.1, ENST00000417443.3
      Conserved Domains (1) summary
      pfam15118
      Location:21 → 77
      DUF4560; Domain of unknown function (DUF4560)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      135421944..135428075
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      133747687..133753818
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0DMW4.1 GenPept UniProtKB/Swiss-Prot:P0DMW4

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials