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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
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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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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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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
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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 Variation Viewer (GRCh37.p13)

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

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