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

Gene ID: 203069, updated on 10-Dec-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, Dec 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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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)

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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