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    SMIM29 small integral membrane protein 29 [ Homo sapiens (human) ]

    Gene ID: 221491, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SMIM29provided by HGNC
    Official Full Name
    small integral membrane protein 29provided by HGNC
    Primary source
    HGNC:HGNC:1340
    See related
    Ensembl:ENSG00000186577 MIM:611419; AllianceGenome:HGNC:1340
    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
    LBH; C6orf1
    Summary
    Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in brain (RPKM 16.6), skin (RPKM 10.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    6p21.31
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (34246395..34249006, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (34070100..34072713, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (34214172..34216783, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene translation initiation factor IF-2-like Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34203963-34204584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17069 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:34211103-34212302 Neighboring gene NFE2L2 motif-containing MPRA enhancer 296 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17070 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17071 Neighboring gene microRNA 6835 Neighboring gene high mobility group AT-hook 1 Neighboring gene ribosomal protein L35 pseudogene 2 Neighboring gene RPS10-NUDT3 readthrough Neighboring gene nudix hydrolase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24380 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:34292259-34292900 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:34294990-34295799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34322011-34322510 Neighboring gene Sharpr-MPRA regulatory region 13549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17073 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17074 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17075

    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. Assignment of a new gene (LBH). Kazmierczak B, et al. Genomics, 1999 Feb 15. PMID 10036196
    2. Identification of 15 loci influencing height in a Korean population. Kim JJ, et al. J Hum Genet, 2010 Jan. PMID 19893584
    3. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. N'Diaye A, et al. PLoS Genet, 2011 Oct. PMID 21998595, Free PMC Article
    4. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. Deng X, et al. PLoS One, 2013. PMID 24324551, Free PMC Article
    5. Identification of host proteins required for HIV infection through a functional genomic screen. Brass AL, et al. Science, 2008 Feb 15. PMID 18187620

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog
    Identification of 15 loci influencing height in a Korean population.
    EBI GWAS Catalog
    Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of chromosome 6 open reading frame 1 (C6orf1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC57858

    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 29
    Names
    uncharacterized protein C6orf1

    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_001008703.4 → NP_001008703.2  small integral membrane protein 29 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AK290164, BU956518
      Consensus CDS
      CCDS4790.2
      UniProtKB/Swiss-Prot
      A0A1C7CYX6, A8K299, Q86T20
      Related
      ENSP00000417604.2, ENST00000476320.6

    2. NM_001008704.4 → NP_001008704.2  small integral membrane protein 29 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 3, which is shorter than isoform 1. Variants 3 and 4 encode the same isoform (3).
      Source sequence(s)
      BC023627, BU956518
      Consensus CDS
      CCDS93896.1
      UniProtKB/TrEMBL
      L8E8G6
      Related
      ENSP00000378441.5, ENST00000394990.8

    3. NM_001287396.3 → NP_001274325.2  small integral membrane protein 29 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 3, which is shorter than isoform 1. Variants 3 and 4 encode the same isoform (3).
      Source sequence(s)
      BU194178, BU956518, CK001844
      Consensus CDS
      CCDS93896.1
      UniProtKB/TrEMBL
      L8E8G6
      Related
      ENSP00000418884.2, ENST00000468145.1

    4. NM_178508.6 → NP_848603.3  small integral membrane protein 29 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      BC047919, BU956518, CK001844
      Consensus CDS
      CCDS4790.2
      UniProtKB/Swiss-Prot
      A0A1C7CYX6, A8K299, Q86T20
      Related
      ENSP00000418062.2, ENST00000481533.5

    RNA

    1. NR_155741.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site in the 5' terminal exon and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BM474526, BU956518
      Related
      ENST00000413013.6

    2. NR_155742.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC009526, BU956518
      Related
      ENST00000637920.1

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      34246395..34249006 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      34070100..34072713 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001287397.1: Suppressed sequence

      Description
      NM_001287397.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    2. NM_001287398.1: Suppressed sequence

      Description
      NM_001287398.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86T20.3 GenPept UniProtKB/Swiss-Prot:Q86T20

    Gene LinkOut

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

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