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    R3HCC1 R3H domain and coiled-coil containing 1 [ Homo sapiens (human) ]

    Gene ID: 203069, updated on 28-Oct-2024

    Summary

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    Official Symbol
    R3HCC1provided by HGNC
    Official Full Name
    R3H domain and coiled-coil containing 1provided by HGNC
    Primary source
    HGNC:HGNC:27329
    See related
    Ensembl:ENSG00000104679 AllianceGenome:HGNC:27329
    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
    Summary
    Predicted to enable nucleic acid binding activity. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in testis (RPKM 16.1), fat (RPKM 12.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See R3HCC1 in Genome Data Viewer
    Location:
    8p21.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (23288092..23296279)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (23562965..23571152)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (23145605..23153792)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene TNFRSF10A 5' regulatory region Neighboring gene TNFRSF10A divergent transcript Neighboring gene NANOG hESC enhancer GRCh37_chr8:23100842-23101343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27114 Neighboring gene MPRA-validated peak6945 silencer Neighboring gene charged multivesicular body protein 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:23129689-23130226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23159094-23159594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23159595-23160095 Neighboring gene lysyl oxidase like 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:23177410-23177975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23182003-23182503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23195830-23196330 Neighboring gene LOXL2 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:23209911-23210493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23236632-23237224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23237225-23237815 Neighboring gene Sharpr-MPRA regulatory region 9444 Neighboring gene Sharpr-MPRA regulatory region 13358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23273382-23273902 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:23279735-23280235 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:23308148-23308855 Neighboring gene Sharpr-MPRA regulatory region 8456 Neighboring gene NANOG hESC enhancer GRCh37_chr8:23312327-23312828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19024

    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. Association between a single nucleotide polymorphism in the R3HCC1 gene and irinotecan toxicity. Kanesada K, et al. Cancer Med, 2023 Feb. PMID 36308049, Free PMC Article
    2. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Lee S, et al. Proc Natl Acad Sci U S A, 2012 Sep 11. PMID 22927429, Free PMC Article
    3. Efficacy of metformin therapy in adolescent girls with androgen excess: relation to sex hormone-binding globulin and androgen receptor polymorphisms. Díaz M, et al. Fertil Steril, 2010 Dec. PMID 20691435
    4. SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay. Kashima I, et al. Genes Dev, 2010 Nov 1. PMID 20930030, Free PMC Article
    5. The RNA binding protein MEX3A promotes tumor progression of breast cancer by post-transcriptional regulation of IGFBP4. Chen W, et al. Breast Cancer Res Treat, 2023 Oct. PMID 37433992, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association between a single nucleotide polymorphism in the R3HCC1 gene and irinotecan toxicity.
      Title: Association between a single nucleotide polymorphism in the R3HCC1 gene and irinotecan toxicity.
    2. Ribosome profiling indicates that this gene can use a non-AUG (CUG) start codon in both human HEK293 and mouse embryonic fibroblast cells.
      Title: Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Efficacy of metformin therapy in adolescent girls with androgen excess: relation to sex hormone-binding globulin and androgen receptor polymorphisms.
    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

    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

    Clone Names

    • DKFZp564N123

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    R3H and coiled-coil domain-containing 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_001136108.3 → NP_001129580.2  R3H and coiled-coil domain-containing protein 1 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      BC032421, BC143829
      Consensus CDS
      CCDS47826.2
      UniProtKB/Swiss-Prot
      B7ZLI1, Q9Y3T6
      UniProtKB/TrEMBL
      A0A0R4J2E2
      Related
      ENSP00000265806.8, ENST00000265806.12
      Conserved Domains (2) summary
      cd02638
      Location:19 → 80
      R3H_unknown_1; R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in ...
      cl17169
      Location:318 → 382
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. NM_001301650.2 → NP_001288579.1  R3H and coiled-coil domain-containing protein 1 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      BC032421, BC143822
      Consensus CDS
      CCDS78317.1
      UniProtKB/TrEMBL
      A0A0D9SF44
      Related
      ENSP00000486278.2, ENST00000625275.3
      Conserved Domains (2) summary
      cd02638
      Location:19 → 80
      R3H_unknown_1; R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in ...
      cl17169
      Location:276 → 340
      RRM_SF; RNA recognition motif (RRM) superfamily

    RNA

    1. NR_125897.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC032421, BC143827

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      23288092..23296279
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      23562965..23571152
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y3T6.3 GenPept UniProtKB/Swiss-Prot:Q9Y3T6

    Gene LinkOut

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

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