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    NCAPD3 non-SMC condensin II complex subunit D3 [ Homo sapiens (human) ]

    Gene ID: 23310, updated on 3-Nov-2024

    Summary

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    Official Symbol
    NCAPD3provided by HGNC
    Official Full Name
    non-SMC condensin II complex subunit D3provided by HGNC
    Primary source
    HGNC:HGNC:28952
    See related
    Ensembl:ENSG00000151503 MIM:609276; AllianceGenome:HGNC:28952
    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
    CAPD3; hcp-6; CAP-D3; MCPH22; hHCP-6; hCAP-D3
    Summary
    Condensin complexes I and II play essential roles in mitotic chromosome assembly and segregation. Both condensins contain 2 invariant structural maintenance of chromosome (SMC) subunits, SMC2 (MIM 605576) and SMC4 (MIM 605575), but they contain different sets of non-SMC subunits. NCAPD3 is 1 of 3 non-SMC subunits that define condensin II (Ono et al., 2003 [PubMed 14532007]).[supplied by OMIM, Mar 2008]
    Expression
    Broad expression in prostate (RPKM 42.0), bone marrow (RPKM 7.1) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NCAPD3 in Genome Data Viewer
    Location:
    11q25
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (134150113..134225461, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (134192253..134267300, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (134020008..134095355, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902797 Neighboring gene junctional adhesion molecule 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133994434-133994972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133994973-133995509 Neighboring gene PTP4A2 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:134027645-134028146 Neighboring gene small nucleolar RNA, C/D box 153 Neighboring gene zinc finger protein 628 pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:134045931-134047130 Neighboring gene MPRA-validated peak1520 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4093 Neighboring gene MPRA-validated peak1521 silencer Neighboring gene MPRA-validated peak1522 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5770 Neighboring gene VPS26 retromer complex component B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4096 Neighboring gene thymocyte nuclear protein 1 Neighboring gene acyl-CoA dehydrogenase family member 8

    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. Knockdown of NCAPD3 inhibits the tumorigenesis of non-small cell lung cancer by regulation of the PI3K/Akt pathway. Yang F, et al. BMC Cancer, 2024 Apr 2. PMID 38566039, Free PMC Article
    2. hCAP-D3 expression marks a prostate cancer subtype with favorable clinical behavior and androgen signaling signature. Lapointe J, et al. Am J Surg Pathol, 2008 Feb. PMID 18223322
    3. Non-SMC condensin I complex subunit D2 and non-SMC condensin II complex subunit D3 induces inflammation via the IKK/NF-κB pathway in ulcerative colitis. Yuan CW, et al. World J Gastroenterol, 2019 Dec 21. PMID 31885422, Free PMC Article
    4. Chromosome-associated protein D3 promotes bacterial clearance in human intestinal epithelial cells by repressing expression of amino acid transporters. Schuster AT, et al. Gastroenterology, 2015 Jun. PMID 25701737, Free PMC Article
    5. The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. Floyd SR, et al. Nature, 2013 Jun 13. PMID 23728299, Free PMC Article

    See all (103) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Knockdown of NCAPD3 inhibits the tumorigenesis of non-small cell lung cancer by regulation of the PI3K/Akt pathway.
      Title: Knockdown of NCAPD3 inhibits the tumorigenesis of non-small cell lung cancer by regulation of the PI3K/Akt pathway.
    2. NCAPD3 promotes prostate cancer progression by up-regulating EZH2 and MALAT1 through STAT3 and E2F1.
      Title: NCAPD3 promotes prostate cancer progression by up-regulating EZH2 and MALAT1 through STAT3 and E2F1.
    3. NCAPD2 and NCAPD3 expression levels have been confirmed to be significantly up-regulated in the intestinal mucosa of patients with active ulcerative colitis. In vitro, the data suggested that silencing NACPD2 and NACPD3 could depress the expression of IL-1beta, IL-6 and TNF-alpha. Further, knockdown of NACPD2 and NACPD3 could remarkably suppress IKK nucleation and NF-kappaB volume.
      Title: Non-SMC condensin I complex subunit D2 and non-SMC condensin II complex subunit D3 induces inflammation via the IKK/NF-κB pathway in ulcerative colitis.
    4. Condensin II(CAP-D3 and CAP-H2) and GAIT subunits associate with L1 RNA in a co-dependent manner, independent of IFN-gamma. These findings suggest that cooperation between the Condensin II and GAIT complexes may facilitate a novel mechanism of L1 repression, thus contributing to the maintenance of genome stability in somatic cells
      Title: Condensin II and GAIT complexes cooperate to restrict LINE-1 retrotransposition in epithelial cells.
    5. CAP-D3 down-regulates transcription of genes that encode amino acid transporters (SLC7A5 and SLC3A2) to promote bacterial autophagy by colon epithelial cells.
      Title: Chromosome-associated protein D3 promotes bacterial clearance in human intestinal epithelial cells by repressing expression of amino acid transporters.
    6. The initial phase of chromosome condensation requires Cdk1-mediated phosphorylation of the CAP-D3 subunit of condensin II.
      Title: The initial phase of chromosome condensation requires Cdk1-mediated phosphorylation of the CAP-D3 subunit of condensin II.
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    8. We show here that protein phosphatase 2A (PP2A), which interacts with condensin II but not condensin I, plays an essential role in targeting condensin II to chromosomes.
      Title: The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A.
    9. hCAP-D3 is a new biomarker for subtype-1 prostate tumors that improves prognostication.
      Title: hCAP-D3 expression marks a prostate cancer subtype with favorable clinical behavior and androgen signaling signature.
    10. The CAP-D3 subunit of the condensin II complex implicated in chromosome assembly and segeregation
      Title: Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells.
    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

    Associated conditions

    Description Tests
    Microcephaly 22, primary, autosomal recessive
    MedGen: C4693834 OMIM: 617984 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study.
    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)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpu vpu HIV-1 Vpu is identified to have a physical interaction with non-SMC condensin II complex, subunit D3 (NCAPD3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ42888, KIAA0056, MGC104671

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in meiotic chromosome condensation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic chromosome condensation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic chromosome condensation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitotic chromosome condensation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of chromosome condensation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of chromosome segregation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of chromosome separation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in condensed chromosome, centromeric region IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in condensed nuclear chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of condensin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of condensin complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of condensin complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in pericentric heterochromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    condensin-2 complex subunit D3

    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_001372065.1 → NP_001358994.1  condensin-2 complex subunit D3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AP001775
      Conserved Domains (2) summary
      sd00044
      Location:542 → 571
      HEAT; HEAT repeat [structural motif]
      pfam12717
      Location:956 → 1120
      Cnd1; non-SMC mitotic condensation complex subunit 1

    2. NM_001372068.1 → NP_001358997.1  condensin-2 complex subunit D3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AP001775
      Consensus CDS
      CCDS91627.1
      UniProtKB/TrEMBL
      A0A8I5KT00
      Related
      ENSP00000510008.1, ENST00000688263.1
      Conserved Domains (2) summary
      sd00044
      Location:542 → 571
      HEAT; HEAT repeat [structural motif]
      pfam12717
      Location:956 → 1120
      Cnd1; non-SMC mitotic condensation complex subunit 1

    3. NM_001372069.1 → NP_001358998.1  condensin-2 complex subunit D3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AP001775
      Conserved Domains (2) summary
      sd00044
      Location:404 → 433
      HEAT; HEAT repeat [structural motif]
      pfam12717
      Location:818 → 982
      Cnd1; non-SMC mitotic condensation complex subunit 1

    4. NM_001372070.1 → NP_001358999.1  condensin-2 complex subunit D3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AP000859, AP001775
      Conserved Domains (2) summary
      sd00044
      Location:404 → 433
      HEAT; HEAT repeat [structural motif]
      pfam12717
      Location:818 → 982
      Cnd1; non-SMC mitotic condensation complex subunit 1

    5. NM_015261.3 → NP_056076.1  condensin-2 complex subunit D3 isoform 1

      See identical proteins and their annotated locations for NP_056076.1

      Status: VALIDATED

      Source sequence(s)
      AP001775
      Consensus CDS
      CCDS31723.1
      UniProtKB/Swiss-Prot
      A6NFS2, P42695, Q4KMQ9
      Related
      ENSP00000433681.3, ENST00000534548.7
      Conserved Domains (2) summary
      sd00044
      Location:542 → 571
      HEAT; HEAT repeat [structural motif]
      pfam12717
      Location:956 → 1120
      Cnd1; non-SMC mitotic condensation complex subunit 1

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      134150113..134225461 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      134192253..134267300 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P42695.2 GenPept UniProtKB/Swiss-Prot:P42695

    Gene LinkOut

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

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