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    SMIM1 small integral membrane protein 1 (Vel blood group) [ Homo sapiens (human) ]

    Gene ID: 388588, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SMIM1provided by HGNC
    Official Full Name
    small integral membrane protein 1 (Vel blood group)provided by HGNC
    Primary source
    HGNC:HGNC:44204
    See related
    Ensembl:ENSG00000235169 MIM:615242; AllianceGenome:HGNC:44204
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Vel
    Summary
    This gene encodes a small, conserved protein that participates in red blood cell formation. The encoded protein is localized to the cell membrane and is the antigen for the Vel blood group. Alternative splicing results in different transcript variants that encode the same protein. [provided by RefSeq, Dec 2013]
    Expression
    Broad expression in testis (RPKM 6.7), bone marrow (RPKM 6.0) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMIM1 in Genome Data Viewer
    Location:
    1p36.32
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3772749..3775956)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (3284345..3287549)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3689313..3692520)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene tumor protein p73 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3661686-3662521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3662522-3663358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 123 Neighboring gene Gfo/Idh/MocA-like oxidoreductase domain containing 3, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3678785-3679286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3679287-3679786 Neighboring gene coiled-coil domain containing 27 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3687696-3688374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3689661-3690176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3690177-3690692 Neighboring gene MPRA functional variant 1:3691528:A:G red blood cell enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3691725-3692240 Neighboring gene RNA, 7SL, cytoplasmic 574, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:3709930-3710608 Neighboring gene leucine rich repeat containing 47 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 125 Neighboring gene Sharpr-MPRA regulatory region 1968 Neighboring gene centrosomal protein 104 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3745882-3747081 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:3747165-3748364 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3755401-3755900 Neighboring gene uncharacterized LOC124903829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3767162-3767662

    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 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. SMIM1 absence is associated with reduced energy expenditure and excess weight. Stefanucci L, et al. Med, 2024 Sep 13. PMID 38906141
    2. SMIM1 missense mutations exert their effect on wild type Vel expression late in erythroid differentiation. van der Rijst MVE, et al. Transfusion, 2021 Jan. PMID 33128268
    3. SMIM1, carrier of the Vel blood group, is a tail-anchored transmembrane protein and readily forms homodimers in a cell-free system. Nylander A, et al. Biosci Rep, 2020 May 29. PMID 32301496, Free PMC Article
    4. Dimerization of small integral membrane protein 1 promotes cell surface presentation of the Vel blood group epitope. Kelley LP, et al. FEBS Lett, 2020 Apr. PMID 31879955
    5. Identification of a novel single-nucleotide mutation in SMIM1 gene that results in low Vel antigen expression. van der Rijst MVE, et al. Transfusion, 2019 Oct. PMID 31218697, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMIM1 absence is associated with reduced energy expenditure and excess weight.
      Title: SMIM1 absence is associated with reduced energy expenditure and excess weight.
    2. SMIM1 missense mutations exert their effect on wild type Vel expression late in erythroid differentiation.
      Title: SMIM1 missense mutations exert their effect on wild type Vel expression late in erythroid differentiation.
    3. Dimerization of small integral membrane protein 1 promotes cell surface presentation of the Vel blood group epitope.
      Title: Dimerization of small integral membrane protein 1 promotes cell surface presentation of the Vel blood group epitope.
    4. SMIM1, carrier of the Vel blood group, is a tail-anchored transmembrane protein and readily forms homodimers in a cell-free system.
      Title: SMIM1, carrier of the Vel blood group, is a tail-anchored transmembrane protein and readily forms homodimers in a cell-free system.
    5. Identification of a novel single-nucleotide mutation in SMIM1 gene that results in low Vel antigen expression.
      Title: Identification of a novel single-nucleotide mutation in SMIM1 gene that results in low Vel antigen expression.
    6. the present study demonstrated that although the SMIM1*64_80del allele is responsible for some variation of Vel phenotype in this donor population, Vel expression is also controlled by molecular changes in SMIM1 intron 2.
      Title: SMIM1 polymorphisms in a donor population from southeast Brazil and their correlation with VEL expression.
    7. rs1175550G and to a lesser extent rs143702418C independently increase SMIM1 and Vel antigen expression.
      Title: SMIM1 variants rs1175550 and rs143702418 independently modulate Vel blood group antigen expression.
    8. Among the 448 samples analysed, 10 (2.23%) harboured the 17 bp deletion of the gene SMIM1, and all were heterozygote for the SMIM1*64_80 del allele.
      Title: Screening for the SMIM1*64_80 del Allele in blood donors in a population from Southern Brazil.
    9. Alleles that initially entered the population have been maintained within the population. The c.64_80del null allele of SMIM1 is one such allele, thus having implications for transfusion medicine and child or maternal health.
      Title: The c.64_80del SMIM1 allele is segregating in the Hutterite population.
    10. SMIM1 carries the Vel antigen as a type II membrane protein with a predicted C-terminal extracellular domain of only 3-12 amino acids
      Title: SMIM1 is a type II transmembrane phosphoprotein and displays the Vel blood group antigen at its carboxyl-terminus.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Vel blood group system
    MedGen: C2745907 OMIM: 615264 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cell surface IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    small integral membrane protein 1
    Names
    bloodgroup VEL protein
    vel blood group antigen

    NCBI Reference Sequences (RefSeq)

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    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.

    Genomic

    1. NG_033869.1 RefSeqGene

      Range
      4989..8196
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_827

    mRNA and Protein(s)

    1. NM_001163724.3 → NP_001157196.1  small integral membrane protein 1

      See identical proteins and their annotated locations for NP_001157196.1

      Status: REVIEWED

      Source sequence(s)
      AL365330
      Consensus CDS
      CCDS57966.1
      UniProtKB/Swiss-Prot
      B2RUZ4
      UniProtKB/TrEMBL
      A0A5Q0LQ04, M4WDD3
      Related
      ENSP00000457386.1, ENST00000444870.7
      Conserved Domains (1) summary
      pfam15875
      Location:3 → 77
      DUF4731; Domain of unknown function (DUF4731)

    2. NM_001288583.2 → NP_001275512.1  small integral membrane protein 1

      See identical proteins and their annotated locations for NP_001275512.1

      Status: REVIEWED

      Source sequence(s)
      AL365330
      Consensus CDS
      CCDS57966.1
      UniProtKB/Swiss-Prot
      B2RUZ4
      UniProtKB/TrEMBL
      A0A5Q0LQ04, M4WDD3
      Related
      ENSP00000496314.2, ENST00000642557.4
      Conserved Domains (1) summary
      pfam15875
      Location:3 → 77
      DUF4731; Domain of unknown function (DUF4731)

    3. NM_001379690.1 → NP_001366619.1  small integral membrane protein 1

      Status: REVIEWED

      Source sequence(s)
      AL365330
      Consensus CDS
      CCDS57966.1
      UniProtKB/Swiss-Prot
      B2RUZ4
      UniProtKB/TrEMBL
      A0A5Q0LQ04, M4WDD3
      Conserved Domains (1) summary
      pfam15875
      Location:3 → 77
      DUF4731; Domain of unknown function (DUF4731)

    4. NM_001379691.1 → NP_001366620.1  small integral membrane protein 1

      Status: REVIEWED

      Source sequence(s)
      AL365330
      Consensus CDS
      CCDS57966.1
      UniProtKB/Swiss-Prot
      B2RUZ4
      UniProtKB/TrEMBL
      A0A5Q0LQ04, M4WDD3
      Conserved Domains (1) summary
      pfam15875
      Location:3 → 77
      DUF4731; Domain of unknown function (DUF4731)

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      3772749..3775956
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420003.1 → XP_047275959.1  small integral membrane protein 1 isoform X1

      UniProtKB/Swiss-Prot
      B2RUZ4
      UniProtKB/TrEMBL
      M4WDD3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      3284345..3287549
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B2RUZ4.1 GenPept UniProtKB/Swiss-Prot:B2RUZ4

    Gene LinkOut

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

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