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

Summary

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

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_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

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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	not available

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 EBI GWAS CatalogPubMed

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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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

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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

SHGC-111172 (e-PCR)
- UniSTS:168194

SHGC-150869 (e-PCR)
- UniSTS:173575

RH17433 (e-PCR)
- UniSTS:50959

RH25290 (e-PCR)
- UniSTS:91158

SHGC-106782 (e-PCR)
- UniSTS:170033

G06763 (e-PCR)
- UniSTS:42297

D11S4440 (e-PCR)
- UniSTS:154720

SHGC-34635 (e-PCR)
- UniSTS:872

RH70189 (e-PCR)
- UniSTS:34965

D11S4125 (e-PCR), detects polymorphism
- UniSTS:42395

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 more info	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)

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
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
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
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
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