U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

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

    Gene ID: 643008, updated on 10-Dec-2024

    Summary

    Go to the top of the page Help
    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 located in membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in stomach (RPKM 3.8), kidney (RPKM 3.7) and 19 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See SMIM5 in Genome Data Viewer
    Location:
    17q25.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (75633434..75641406)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (76526621..76534593)
    RS_2024_09 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 endoregulin

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    small integral membrane protein 5

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_2024_08

    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.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools