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    Smim1 small integral membrane protein 1 (Vel blood group) [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500595, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Smim1provided by RGD
    Official Full Name
    small integral membrane protein 1 (Vel blood group)provided by RGD
    Primary source
    RGD:1564257
    See related
    EnsemblRapid:ENSRNOG00000080057 AllianceGenome:RGD:1564257
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1564257
    Summary
    Predicted to enable protein homodimerization activity. Predicted to be located in cell surface and plasma membrane. Orthologous to human SMIM1 (small integral membrane protein 1 (Vel blood group)). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 319.7), Lung (RPKM 118.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Smim1 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (169861751..169867070, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (164579327..164584650, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (171306836..171312109, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene DNA fragmentation factor subunit beta Neighboring gene centrosomal protein 104 Neighboring gene leucine rich repeat containing 47 Neighboring gene uncharacterized LOC120103048 Neighboring gene coiled-coil domain containing 27 Neighboring gene uncharacterized LOC102551562 Neighboring gene uncharacterized LOC134479057

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. SMIM1 is a type II transmembrane phosphoprotein and displays the Vel blood group antigen at its carboxyl-terminus. Arnaud L, et al. FEBS Lett, 2015 Nov 30. PMID 26452714, Free PMC Article
    2. Homozygosity for a null allele of SMIM1 defines the Vel-negative blood group phenotype. Storry JR, et al. Nat Genet, 2013 May. PMID 23563606
    3. Disruption of SMIM1 causes the Vel- blood type. Ballif BA, et al. EMBO Mol Med, 2013 May. PMID 23505126, Free PMC Article
    4. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. Prunotto M, et al. J Proteomics, 2013 Apr 26. PMID 23376485
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    small integral membrane protein 1

    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_001163723.1 → NP_001157195.1  small integral membrane protein 1

      See identical proteins and their annotated locations for NP_001157195.1

      Status: VALIDATED

      Source sequence(s)
      CB698087, CB775577, CB786874
      UniProtKB/TrEMBL
      A6IUK2
      Related
      ENSRNOP00000101509.1, ENSRNOT00000168662.1
      Conserved Domains (1) summary
      pfam15875
      Location:3 → 77
      DUF4731; Domain of unknown function (DUF4731)

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      169861751..169867070 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006239509.5 → XP_006239571.1  small integral membrane protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006239571.1

      UniProtKB/TrEMBL
      A6IUK2
      Conserved Domains (1) summary
      pfam15875
      Location:3 → 77
      DUF4731; Domain of unknown function (DUF4731)

    2. XM_039110655.2 → XP_038966583.1  small integral membrane protein 1 isoform X1

      UniProtKB/TrEMBL
      A6IUK2
      Conserved Domains (1) summary
      pfam15875
      Location:3 → 77
      DUF4731; Domain of unknown function (DUF4731)

    3. XM_006239508.5 → XP_006239570.1  small integral membrane protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006239570.1

      UniProtKB/TrEMBL
      A6IUK2
      Conserved Domains (1) summary
      pfam15875
      Location:3 → 77
      DUF4731; Domain of unknown function (DUF4731)

    4. XM_039110654.2 → XP_038966582.1  small integral membrane protein 1 isoform X1

      UniProtKB/TrEMBL
      A6IUK2
      Conserved Domains (1) summary
      pfam15875
      Location:3 → 77
      DUF4731; Domain of unknown function (DUF4731)
    Nucleotide Protein Strain
    Heading Accession and Version

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