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

Gene ID: 26093, updated on 14-Sep-2025
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, Jul 2025]
Expression
Ubiquitous expression in testis (RPKM 10.3), bone marrow (RPKM 8.8) and 25 other tissues See more
Orthologs
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See CCDC9 in Genome Data Viewer
Location:
19q13.32
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (47256525..47275723)
RS_2025_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

Go to nucleotide: Graphics FASTA GenBank

  • 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

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. CircNFATC3 promotes the proliferation of gastric cancer through binding to IGF2BP3 and restricting its ubiquitination to enhance CCND1 mRNA stability. Yang F, et al. J Transl Med, 2023 Jun 20. PMID 37340423, Free PMC Article
  5. 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

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

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 
Preferred Names
coiled-coil domain-containing protein 9

NEW Try the new Transcript table

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_2025_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

    UniProtKB/TrEMBL
    B4DXW2
    Related
    ENSP00000521127.1, ENST00000851059.1

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

    UniProtKB/TrEMBL
    A0A2R8Y4Z8, B4DXW2
    Related
    ENSP00000494410.1, ENST00000643617.1

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

    UniProtKB/TrEMBL
    A0A2R8Y4Z8, B4DXW2

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

    UniProtKB/TrEMBL
    A0A2R8Y4Z8, B4DXW2

  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
    UniProtKB/TrEMBL
    B4DXW2
    Related
    ENSP00000627368.1, ENST00000957309.1

  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

    UniProtKB/TrEMBL
    B4DXW2

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

    UniProtKB/TrEMBL
    B4DXW2
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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