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

    Gene ID: 91433, updated on 27-Nov-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, Nov 2024]
    Expression
    Ubiquitous expression in skin (RPKM 2.9), colon (RPKM 2.1) and 25 other tissues See more
    Orthologs
    mouse all
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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

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

      UniProtKB/Swiss-Prot
      A6NED2, B2RTP9, Q29RX6

    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

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

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

    Gene LinkOut

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

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