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RCCD1 RCC1 domain containing 1 [ Homo sapiens (human) ]

Gene ID: 91433, updated on 10-Dec-2024

Summary

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Official Symbol
RCCD1provided by HGNC
Official Full Name
RCC1 domain containing 1provided by HGNC
Primary source
HGNC:HGNC:30457
See related
Ensembl:ENSG00000166965 MIM:617997; AllianceGenome:HGNC:30457
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 be involved in chromatin organization. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Dec 2024]
Expression
Ubiquitous expression in skin (RPKM 2.9), colon (RPKM 2.1) and 25 other tissues See more
Orthologs
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Genomic context

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See RCCD1 in Genome Data Viewer
Location:
15q26.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (90954884..90963125)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (88714467..88722708)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (91498114..91506355)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6833 Neighboring gene unc-45 myosin chaperone A Neighboring gene HD domain containing 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:91496471-91496971 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:91497796-91498350 Neighboring gene RCCD1 and UNC45A antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6834 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6836 Neighboring gene PRC1 antisense RNA 1 Neighboring gene protein regulator of cytokinesis 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:91526592-91527791 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:91537071-91537938 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:91537939-91538805 Neighboring gene uncharacterized LOC124903556

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. RCCD1 depletion attenuates TGF-β-induced EMT and cell migration by stabilizing cytoskeletal microtubules in NSCLC cells. Wu J, et al. Cancer Lett, 2017 Aug 1. PMID 28455245
  2. Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk. Hoffman JD, et al. PLoS Genet, 2017 Mar. PMID 28362817, Free PMC Article
  3. LINC01419 promotes cell proliferation and metastasis in lung adenocarcinoma via sponging miR-519b-3p to up-regulate RCCD1. Cheng Z, et al. Biochem Biophys Res Commun, 2019 Nov 26. PMID 31582214
  4. JMJD5 is a human arginyl C-3 hydroxylase. Wilkins SE, et al. Nat Commun, 2018 Mar 21. PMID 29563586, Free PMC Article
  5. Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.1. Cai Q, et al. Nat Genet, 2014 Aug. PMID 25038754, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. miR-519b-3p binds to LINC01419 and has a role in upregulating RCCD1 in lung adenocarcinoma cells
    Title: LINC01419 promotes cell proliferation and metastasis in lung adenocarcinoma via sponging miR-519b-3p to up-regulate RCCD1.
  2. JMJD5 catalyzes stereoselective C-3 hydroxylation of arginine residues in sequences from human RCCD1 and ribosomal protein S6.
    Title: JMJD5 is a human arginyl C-3 hydroxylase.
  3. RCCD1 as a novel regulator of TGF-beta-induced epithelial mesenchymal transformation and cell migration in non-small lung carcinoma cells.
    Title: RCCD1 depletion attenuates TGF-β-induced EMT and cell migration by stabilizing cytoskeletal microtubules in NSCLC cells.
  4. Expression of RCCD1 in whole blood was also suggestively associated with disease risk (p-value: 1.2x10-05), as were expression of ACAP1 (p-value: 1.9x10-05) and LRRC25 (p-value: 5.2x10-05). While genome-wide association studies (GWAS) have implicated RCCD1 and ANKLE1 in breast cancer risk, they have not identified the remaining three genes
    Title: Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk.
  5. RCCD1 and KDM8 form a histone demethylase complex.
    Title: Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation.
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 analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.1.
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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC14386

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
RCC1 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_001017919.2 → NP_001017919.1  RCC1 domain-containing protein 1

    See identical proteins and their annotated locations for NP_001017919.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AA564459, AL527085, BC008845, BQ924078, BU850147
    Consensus CDS
    CCDS32333.1
    UniProtKB/Swiss-Prot
    A6NED2, B2RTP9, Q29RX6
    UniProtKB/TrEMBL
    G3V2I3
    Related
    ENSP00000377801.2, ENST00000394258.7
    Conserved Domains (2) summary
    COG5184
    Location:156 → 340
    ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
    pfam00415
    Location:319 → 366
    RCC1; Regulator of chromosome condensation (RCC1) repeat

  2. NM_033544.3 → NP_291022.2  RCC1 domain-containing protein 1

    See identical proteins and their annotated locations for NP_291022.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AA564459, AL527085, BC008845, BQ924078, BU850147, BX375216
    Consensus CDS
    CCDS32333.1
    UniProtKB/Swiss-Prot
    A6NED2, B2RTP9, Q29RX6
    UniProtKB/TrEMBL
    G3V2I3
    Related
    ENSP00000451963.1, ENST00000556618.1
    Conserved Domains (2) summary
    COG5184
    Location:156 → 340
    ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
    pfam00415
    Location:319 → 366
    RCC1; Regulator of chromosome condensation (RCC1) repeat

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    90954884..90963125
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047433317.1 → XP_047289273.1  RCC1 domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NED2, B2RTP9, Q29RX6
    UniProtKB/TrEMBL
    G3V2I3

  2. XM_047433316.1 → XP_047289272.1  RCC1 domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NED2, B2RTP9, Q29RX6
    UniProtKB/TrEMBL
    G3V2I3

  3. XM_047433318.1 → XP_047289274.1  RCC1 domain-containing protein 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    88714467..88722708
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379173.1 → XP_054235148.1  RCC1 domain-containing protein 1 isoform X2

  2. XM_054379172.1 → XP_054235147.1  RCC1 domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NED2, B2RTP9, Q29RX6
    UniProtKB/TrEMBL
    G3V2I3

  3. XM_054379171.1 → XP_054235146.1  RCC1 domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NED2, B2RTP9, Q29RX6
    UniProtKB/TrEMBL
    G3V2I3
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A6NED2.1 GenPept UniProtKB/Swiss-Prot:A6NED2

Gene LinkOut

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