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    SMIM27 small integral membrane protein 27 [ Homo sapiens (human) ]

    Gene ID: 100129250, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SMIM27provided by HGNC
    Official Full Name
    small integral membrane protein 27provided by HGNC
    Primary source
    HGNC:HGNC:31420
    See related
    Ensembl:ENSG00000235453 AllianceGenome:HGNC:31420
    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
    C9orf133; TOPORS-AS1
    Summary
    Predicted to be located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 2.9), spleen (RPKM 1.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMIM27 in Genome Data Viewer
    Location:
    9p21.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (32551144..32566860)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (32567306..32583045)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (32551142..32566858)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101060445 Neighboring gene uncharacterized LOC124902138 Neighboring gene RNA sensor RIG-I Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:32508078-32508796 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:32508797-32509513 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28262 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19827 Neighboring gene H3K27ac hESC enhancers GRCh37_chr9:32551644-32552358 and GRCh37_chr9:32552359-32553072 Neighboring gene TOP1 binding arginine/serine rich protein, E3 ubiquitin ligase Neighboring gene NADH:ubiquinone oxidoreductase subunit B6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28266 Neighboring gene DNA fragmentation factor subunit beta pseudogene 1 Neighboring gene uncharacterized LOC105376015 Neighboring gene TATA-box binding protein associated factor 1 like

    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. Pervasive functional translation of noncanonical human open reading frames. Chen J, et al. Science, 2020 Mar 6. PMID 32139545, Free PMC Article
    2. Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. Kennedy RB, et al. Hum Genet, 2012 Sep. PMID 22610502, Free PMC Article
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ25547

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    small integral membrane protein 27
    Names
    TOPORS antisense RNA 1 (non-protein coding)

    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_001349118.1 → NP_001336047.1  small integral membrane protein 27

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the functional protein. Variants 1, 2, and 5 encode the same protein.
      Source sequence(s)
      AL353671, CB048380
      Consensus CDS
      CCDS87647.1
      UniProtKB/Swiss-Prot
      A0A1B0GUW7
      UniProtKB/TrEMBL
      A0A1B0GW09
      Related
      ENSP00000490275.1, ENST00000453396.5

    2. NM_001349119.2 → NP_001336048.1  small integral membrane protein 27

      Status: VALIDATED

      Description
      Transcript Variant: This variant differs in the 5' UTR compared to variant 1. Variants 1, 2, and 5 encode the same protein.
      Source sequence(s)
      AL353671, CB048380, HY032383
      Consensus CDS
      CCDS87647.1
      UniProtKB/Swiss-Prot
      A0A1B0GUW7
      UniProtKB/TrEMBL
      A0A1B0GW09
      Related
      ENSP00000490727.2, ENST00000450093.3

    3. NM_001387564.1 → NP_001374493.1  small integral membrane protein 27

      Status: VALIDATED

      Source sequence(s)
      AL353671
      Consensus CDS
      CCDS87647.1
      UniProtKB/Swiss-Prot
      A0A1B0GUW7
      UniProtKB/TrEMBL
      A0A1B0GW09
      Related
      ENSP00000508648.1, ENST00000692500.1

    RNA

    1. NR_146061.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks a 5' exon and uses an alternate 3' exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BI916035, DA702677, HY032383
      Related
      ENST00000425533.1

    2. NR_146063.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks a 5' exon and uses an alternate 3' exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BI916035, DA753662, HY032383

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      32551144..32566860
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      32567306..32583045
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A0A1B0GUW7.1 GenPept UniProtKB/Swiss-Prot:A0A1B0GUW7

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials