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    WASHC3 WASH complex subunit 3 [ Homo sapiens (human) ]

    Gene ID: 51019, updated on 14-Nov-2024

    Summary

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    Official Symbol
    WASHC3provided by HGNC
    Official Full Name
    WASH complex subunit 3provided by HGNC
    Primary source
    HGNC:HGNC:24256
    See related
    Ensembl:ENSG00000120860 MIM:619925; AllianceGenome:HGNC:24256
    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
    CCDC53; CGI-116
    Summary
    Predicted to be involved in actin filament polymerization and exocytosis. Part of WASH complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 48.2), adrenal (RPKM 16.9) and 24 other tissues See more
    Orthologs
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    Genomic context

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    See WASHC3 in Genome Data Viewer
    Location:
    12q23.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (102012840..102062124, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (101973971..102023257, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (102406618..102455902, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6874 Neighboring gene Sharpr-MPRA regulatory region 5561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6876 Neighboring gene ribosomal protein L9 pseudogene 24 Neighboring gene uncharacterized LOC107984548 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22809 Neighboring gene neudesin neurotrophic factor pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6878 Neighboring gene nucleoporin 37 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6879 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:102514807-102515364 Neighboring gene PARP1 binding protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:102546739-102547240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6880 Neighboring gene pro-melanin concentrating hormone

    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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    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of coiled-coil domain containing 53 (CCDC53) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N 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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    Homology

    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 actin filament polymerization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endosomal transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of Arp2/3 complex-mediated actin nucleation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of WASH complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of WASH complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of WASH complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in early endosome membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    WASH complex subunit 3
    Names
    WASH complex subunit CCDC53
    coiled-coil domain containing 53
    coiled-coil domain-containing protein 53

    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_001301107.1 → NP_001288036.1  WASH complex subunit 3 isoform 2

      See identical proteins and their annotated locations for NP_001288036.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC079907, BX356987, DB452335
      Consensus CDS
      CCDS73512.1
      UniProtKB/TrEMBL
      F5GXZ7, F5GZ97
      Related
      ENSP00000443857.1, ENST00000545679.5
      Conserved Domains (1) summary
      pfam10152
      Location:30 → 166
      CCDC53; Subunit CCDC53 of WASH complex

    2. NM_016053.4 → NP_057137.1  WASH complex subunit 3 isoform 1

      See identical proteins and their annotated locations for NP_057137.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC079907, AF151874
      Consensus CDS
      CCDS44959.1
      UniProtKB/Swiss-Prot
      B2RC74, Q53FF0, Q6IAI4, Q96QK0, Q9Y3C0
      UniProtKB/TrEMBL
      F5GXZ7
      Related
      ENSP00000240079.6, ENST00000240079.11
      Conserved Domains (1) summary
      pfam10152
      Location:30 → 167
      CCDC53; Subunit CCDC53 of WASH complex

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      102012840..102062124 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024448998.2 → XP_024304766.1  WASH complex subunit 3 isoform X4

      Conserved Domains (1) summary
      pfam10152
      Location:18 → 133
      DUF2360; Predicted coiled-coil domain-containing protein (DUF2360)

    2. XM_017019383.2 → XP_016874872.1  WASH complex subunit 3 isoform X3

    3. XM_047428921.1 → XP_047284877.1  WASH complex subunit 3 isoform X2

    4. XM_011538423.2 → XP_011536725.1  WASH complex subunit 3 isoform X1

      UniProtKB/TrEMBL
      F5GWI9, F5GXZ7
      Related
      ENSP00000441810.1, ENST00000540536.5
      Conserved Domains (1) summary
      pfam10152
      Location:30 → 167
      DUF2360; Predicted coiled-coil domain-containing protein (DUF2360)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      101973971..102023257 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372163.1 → XP_054228138.1  WASH complex subunit 3 isoform X4

    2. XM_054372162.1 → XP_054228137.1  WASH complex subunit 3 isoform X3

    3. XM_054372161.1 → XP_054228136.1  WASH complex subunit 3 isoform X2

    4. XM_054372160.1 → XP_054228135.1  WASH complex subunit 3 isoform X1

      UniProtKB/TrEMBL
      F5GWI9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y3C0.1 GenPept UniProtKB/Swiss-Prot:Q9Y3C0

    Gene LinkOut

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

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