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    CCDC9 coiled-coil domain containing 9 [ Homo sapiens (human) ]

    Gene ID: 26093, updated on 3-Nov-2024

    Summary

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    Official Symbol
    CCDC9provided by HGNC
    Official Full Name
    coiled-coil domain containing 9provided by HGNC
    Primary source
    HGNC:HGNC:24560
    See related
    Ensembl:ENSG00000105321 AllianceGenome:HGNC:24560
    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
    Enables RNA binding activity. Part of exon-exon junction complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 10.3), bone marrow (RPKM 8.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CCDC9 in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (47256525..47275723)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (50081834..50097265)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (47759782..47775210)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47730339-47731281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14861 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:47735673-47736296 Neighboring gene BCL2 binding component 3 Neighboring gene microRNA 3190 Neighboring gene microRNA 3191 Neighboring gene uncharacterized LOC124904731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47744377-47745178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14864 Neighboring gene CRISPRi-validated cis-regulatory element chr19.5064 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47759131-47760040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10849 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47769923-47770422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10851 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10852 Neighboring gene CRISPRi-validated cis-regulatory element chr19.5070 Neighboring gene InaF motif containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47793125-47793976 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:47818477-47818672 Neighboring gene Sharpr-MPRA regulatory region 10427 Neighboring gene complement C5a receptor 1 Neighboring gene Sharpr-MPRA regulatory region 4678 Neighboring gene complement C5a receptor 2

    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. CCDC9 is identified as a novel candidate gene of severe asthenozoospermia. Sha Y, et al. Syst Biol Reprod Med, 2019 Dec. PMID 31502483
    2. hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. Drew K, et al. Mol Syst Biol, 2021 May. PMID 33973408, Free PMC Article
    3. Myristoylated alanine-rich C-kinase substrate effector domain phosphorylation regulates the growth and radiation sensitization of glioblastoma. Eustace NJ, et al. Int J Oncol, 2019 Jun. PMID 30942445, Free PMC Article
    4. Nsp2 has the potential to be a drug target revealed by global identification of SARS-CoV-2 Nsp2-interacting proteins. Zheng YX, et al. Acta Biochim Biophys Sin (Shanghai), 2021 Aug 31. PMID 34159380
    5. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Singh G, et al. Cell, 2012 Nov 9. PMID 23084401, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    • DKFZp586M1019

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of exon-exon junction complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 9

    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_015603.3 → NP_056418.1  coiled-coil domain-containing protein 9

      See identical proteins and their annotated locations for NP_056418.1

      Status: VALIDATED

      Source sequence(s)
      AK302153, AL050284, BC009743, BM737911, CR977312
      Consensus CDS
      CCDS12698.1
      UniProtKB/Swiss-Prot
      Q9Y3X0
      UniProtKB/TrEMBL
      B4DXW2
      Related
      ENSP00000221922.5, ENST00000221922.11
      Conserved Domains (2) summary
      pfam15266
      Location:219 → 373
      DUF4594; Domain of unknown function (DUF4594)
      cl26386
      Location:305 → 483
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      47256525..47275723
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438583.1 → XP_047294539.1  coiled-coil domain-containing protein 9 isoform X2

    2. XM_047438580.1 → XP_047294536.1  coiled-coil domain-containing protein 9 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y4Z8
      Related
      ENSP00000494410.1, ENST00000643617.1

    3. XM_047438582.1 → XP_047294538.1  coiled-coil domain-containing protein 9 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y4Z8

    4. XM_047438581.1 → XP_047294537.1  coiled-coil domain-containing protein 9 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y4Z8

    5. XM_047438585.1 → XP_047294541.1  coiled-coil domain-containing protein 9 isoform X4

    6. XM_047438584.1 → XP_047294540.1  coiled-coil domain-containing protein 9 isoform X3

      UniProtKB/Swiss-Prot
      Q9Y3X0

    7. XM_017026578.2 → XP_016882067.1  coiled-coil domain-containing protein 9 isoform X3

      UniProtKB/Swiss-Prot
      Q9Y3X0
      UniProtKB/TrEMBL
      B4DXW2
      Conserved Domains (2) summary
      pfam15266
      Location:219 → 373
      DUF4594; Domain of unknown function (DUF4594)
      cl26386
      Location:305 → 483
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

    8. XM_047438586.1 → XP_047294542.1  coiled-coil domain-containing protein 9 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      50081834..50097265
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320495.1 → XP_054176470.1  coiled-coil domain-containing protein 9 isoform X3

    2. XM_054320496.1 → XP_054176471.1  coiled-coil domain-containing protein 9 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y3X0.1 GenPept UniProtKB/Swiss-Prot:Q9Y3X0

    Gene LinkOut

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

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