Human Gene NCAPD3 (ENST00000534548.7_11) from GENCODE V47lift37
  Description: non-SMC condensin II complex subunit D3, transcript variant 1 (from RefSeq NM_015261.3)
Gencode Transcript: ENST00000534548.7_11
Gencode Gene: ENSG00000151503.14_16
Transcript (Including UTRs)
   Position: hg19 chr11:134,020,008-134,093,861 Size: 73,854 Total Exon Count: 35 Strand: -
Coding Region
   Position: hg19 chr11:134,022,839-134,093,820 Size: 70,982 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:134,020,008-134,093,861)mRNA (may differ from genome)Protein (1498 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CNDD3_HUMAN
DESCRIPTION: RecName: Full=Condensin-2 complex subunit D3; AltName: Full=Non-SMC condensin II complex subunit D3; Short=hCAP-D3;
FUNCTION: Regulatory subunit of the condensin-2 complex, a complex which establishes mitotic chromosome architecture and is involved in physical rigidity of the chromatid axis.
SUBUNIT: Component of the condensin-2 complex, which contains the SMC2 and SMC4 heterodimer, and 3 non SMC subunits that probably regulate the complex: NCAPH2, NCAPD3 and NCAPG2.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Contains 4 HEAT repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.32 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 141.35 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -13.0041-0.317 Picture PostScript Text
3' UTR -867.702831-0.306 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR026971 - CND1/NCAPD3
IPR026003 - Cohesin_HEAT
IPR012371 - NCAPD3

Pfam Domains:
PF12717 - non-SMC mitotic condensation complex subunit 1
PF12765 - HEAT repeat associated with sister chromatid cohesion

SCOP Domains:
48371 - ARM repeat
48431 - Lipovitellin-phosvitin complex, superhelical domain
48464 - ENTH/VHS domain

ModBase Predicted Comparative 3D Structure on P42695
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0035064 methylated histone binding

Biological Process:
GO:0007049 cell cycle
GO:0007076 mitotic chromosome condensation
GO:0010032 meiotic chromosome condensation
GO:0030261 chromosome condensation
GO:0051301 cell division
GO:0051304 chromosome separation

Cellular Component:
GO:0000779 condensed chromosome, centromeric region
GO:0000799 nuclear condensin complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016020 membrane
GO:0031618 nuclear pericentric heterochromatin


-  Descriptions from all associated GenBank mRNAs
  AK124878 - Homo sapiens cDNA FLJ42888 fis, clone BRHIP3008183.
BC098398 - Homo sapiens non-SMC condensin II complex, subunit D3, mRNA (cDNA clone MGC:104671 IMAGE:30528692), complete cds.
D29954 - Homo sapiens KIAA0056 mRNA.
BC144524 - Homo sapiens cDNA clone IMAGE:9053051.
AK025549 - Homo sapiens cDNA: FLJ21896 fis, clone HEP03441.
AF070553 - Homo sapiens clone 24782 unknown mRNA.
BC011408 - Homo sapiens non-SMC condensin II complex, subunit D3, mRNA (cDNA clone IMAGE:3870709), partial cds.
AK025667 - Homo sapiens cDNA: FLJ22014 fis, clone HEP07365.
AK095267 - Homo sapiens cDNA FLJ37948 fis, clone CTONG2009132.
JD327414 - Sequence 308438 from Patent EP1572962.
JD527280 - Sequence 508304 from Patent EP1572962.
JD507412 - Sequence 488436 from Patent EP1572962.
JD056723 - Sequence 37747 from Patent EP1572962.
JD254041 - Sequence 235065 from Patent EP1572962.
JD339815 - Sequence 320839 from Patent EP1572962.
JD415344 - Sequence 396368 from Patent EP1572962.
JD397352 - Sequence 378376 from Patent EP1572962.
JD419025 - Sequence 400049 from Patent EP1572962.
JD392181 - Sequence 373205 from Patent EP1572962.
KJ902323 - Synthetic construct Homo sapiens clone ccsbBroadEn_11717 NCAPD3 gene, encodes complete protein.
DQ592422 - Homo sapiens piRNA piR-59534, complete sequence.
JD482164 - Sequence 463188 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P42695 (Reactome details) participates in the following event(s):

R-HSA-2172666 RB1 binds condensin II
R-HSA-2288097 Condensin II complex binds H4K20me1-containing nucleosomes
R-HSA-2429719 MCPH1 sequesters condensin II
R-HSA-2294600 CDK1 phosphorylates condensin II subunit NCAPD3
R-HSA-2294580 PLK1 hyperphosphorylates Condensin II complex
R-HSA-2294590 PLK1 binds phosphorylated condensin II complex
R-HSA-2299718 Condensation of Prophase Chromosomes
R-HSA-68875 Mitotic Prophase
R-HSA-68886 M Phase
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: A6NFS2, CAPD3, CNDD3_HUMAN, ENST00000534548.1, ENST00000534548.2, ENST00000534548.3, ENST00000534548.4, ENST00000534548.5, ENST00000534548.6, KIAA0056, NCAPD3 , NM_015261, P42695, Q4KMQ9, uc324nag.1, uc324nag.2
UCSC ID: ENST00000534548.7_11
RefSeq Accession: NM_015261.3
Protein: P42695 (aka CNDD3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.