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SMIM5 small integral membrane protein 5 [ Homo sapiens (human) ]

Gene ID: 643008, updated on 5-Mar-2024

Summary

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Official Symbol
SMIM5provided by HGNC
Official Full Name
small integral membrane protein 5provided by HGNC
Primary source
HGNC:HGNC:40030
See related
Ensembl:ENSG00000204323 AllianceGenome:HGNC:40030
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
PP12104; C17orf109
Summary
Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in stomach (RPKM 3.8), kidney (RPKM 3.7) and 19 other tissues See more
Orthologs
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Genomic context

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See SMIM5 in Genome Data Viewer
Location:
17q25.1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (75633434..75641406)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (76526621..76534593)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73629514..73637486)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8971 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:73521300-73521484 Neighboring gene LLGL scribble cell polarity complex component 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73537609-73538426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73540787-73541589 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73548510-73549090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73553000-73553936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73553937-73554872 Neighboring gene Sharpr-MPRA regulatory region 3602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12769 Neighboring gene Sharpr-MPRA regulatory region 12965 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73583697-73584530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73584531-73585362 Neighboring gene myosin XVB Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73628586-73629266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73629267-73629946 Neighboring gene RecQ like helicase 5 Neighboring gene Sharpr-MPRA regulatory region 461 Neighboring gene HNF1 motif-containing MPRA enhancer 181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12771 Neighboring gene uncharacterized LOC107985013 Neighboring gene small integral membrane protein 6

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. FUT11 as a potential biomarker of clear cell renal cell carcinoma progression based on meta-analysis of gene expression data. Zodro E, et al. Tumour Biol, 2014 Mar. PMID 24318988, Free PMC Article
  2. 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
  3. A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. Yao Z, et al. Mol Cell, 2017 Jan 19. PMID 28065597, Free PMC Article
  4. RIG-I regulates myeloid differentiation by promoting TRIM25-mediated ISGylation. Wu SF, et al. Proc Natl Acad Sci U S A, 2020 Jun 23. PMID 32513696, Free PMC Article
  5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

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

Clone Names

  • FLJ31206, DKFZp451K2118

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 5

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_001162995.3 → NP_001156467.1  small integral membrane protein 5

    See identical proteins and their annotated locations for NP_001156467.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the functional protein.
    Source sequence(s)
    BC027861, BI712658, CA413024
    Consensus CDS
    CCDS54165.1
    UniProtKB/Swiss-Prot
    Q71RC9
    Related
    ENSP00000364363.3, ENST00000375215.3
    Conserved Domains (1) summary
    pfam15831
    Location:8 → 57
    DUF4713; Domain of unknown function (DUF4713)

RNA

  1. NR_028439.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate 5' end, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC087749, AK055768, AL832643, CA413024

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
    75633434..75641406
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047436530.1 → XP_047292486.1  small integral membrane protein 5 isoform X3

    UniProtKB/Swiss-Prot
    Q71RC9

  2. XM_047436531.1 → XP_047292487.1  small integral membrane protein 5 isoform X3

    UniProtKB/Swiss-Prot
    Q71RC9

  3. XM_017024944.2 → XP_016880433.1  small integral membrane protein 5 isoform X1

  4. XM_017024945.3 → XP_016880434.1  small integral membrane protein 5 isoform X2

  5. XM_017024947.3 → XP_016880436.1  small integral membrane protein 5 isoform X3

    UniProtKB/Swiss-Prot
    Q71RC9
    Conserved Domains (1) summary
    pfam15831
    Location:8 → 57
    DUF4713; Domain of unknown function (DUF4713)

  6. XM_011525119.3 → XP_011523421.1  small integral membrane protein 5 isoform X3

    See identical proteins and their annotated locations for XP_011523421.1

    UniProtKB/Swiss-Prot
    Q71RC9
    Related
    ENSP00000477017.1, ENST00000537494.1
    Conserved Domains (1) summary
    pfam15831
    Location:8 → 57
    DUF4713; Domain of unknown function (DUF4713)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    76526621..76534593
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316907.1 → XP_054172882.1  small integral membrane protein 5 isoform X3

    UniProtKB/Swiss-Prot
    Q71RC9

  2. XM_054316909.1 → XP_054172884.1  small integral membrane protein 5 isoform X3

    UniProtKB/Swiss-Prot
    Q71RC9

  3. XM_054316908.1 → XP_054172883.1  small integral membrane protein 5 isoform X4

  4. XM_054316906.1 → XP_054172881.1  small integral membrane protein 5 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_015452.1: Suppressed sequence

    Description
    NR_015452.1: This RefSeq was permanently suppressed because it is now thought that this gene does encode a protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q71RC9.2 GenPept UniProtKB/Swiss-Prot:Q71RC9

Gene LinkOut

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

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