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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
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Genomic context

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See SMIM29 in Genome Data Viewer
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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