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

Gene ID: 100129250, updated on 8-Mar-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 integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 2.9), spleen (RPKM 1.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
9p21.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (32551144..32566860)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (32567306..32583045)
105.20220307 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)

Genotypes

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_2023_10

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

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Molecular Biology Databases
Research Materials