Summary page for 'CDCA3' (ENSG00000111665) - Project: IRS

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Basic Gene Stats

Species: Human
Gene Name: 'CDCA3' (HUGO: CDCA3)
ALEXA Gene ID: 4000 (ALEXA_hs_53_36o)
EnsEMBL Gene ID: ENSG00000111665
Entrez Gene Record(s): CDCA3
Ensembl Gene Record: ENSG00000111665
Evidence: Known Gene
Gene Type: protein_coding
Location: chr12 6828262-6830686 (-): 12p13
Size (bp): 2425
Description: Cell division cycle-associated protein 3 (Trigger of mitotic entry protein 1)(TOME-1)(Gene-rich cluster protein C8) [Source:UniProtKB/Swiss-Prot;Acc:Q99618]

Data links for each library (displays expression data in UCSC Genome Browser)

SUM149_DMSO (1188 total reads for 'CDCA3'). UCSC data links: (C | P)
SUM149_IR (867 total reads for 'CDCA3'). UCSC data links: (C | P)
A431_DMSO (970 total reads for 'CDCA3'). UCSC data links: (C | P)
A431_IR (299 total reads for 'CDCA3'). UCSC data links: (C | P)
PC9_DMSO (285 total reads for 'CDCA3'). UCSC data links: (C | P)
PC9_IR (329 total reads for 'CDCA3'). UCSC data links: (C | P)

Link to other genes in the same chromosome region as 'CDCA3'


Features defined for this gene: 53

Gene: 1
Transcript: 1
ExonRegion: 6
Junction: 15
    KnownJunction: 5
    NovelJunction: 10
Boundary: 10
    KnownBoundary: 0
    NovelBoundary: 10
Intron: 5
ActiveIntronRegion: 7
SilentIntronRegion: 2
Intergenic: 2
ActiveIntergenicRegion: 4
SilentIntergenicRegion: 1

Summary of transcript specific features for 'CDCA3' (ENSG00000111665)

ENST00000229265:ER1a, E1a_E2a, ER2a, E2a_E3a, ER3a, E3a_E4a, ER4a, E4a_E5a, ER5a, E5a_E6a, ER6a

Summary of known expressed features

Expressed above background

LibraryExon Regions
Known Junctions

Detected at any level above 0

LibraryExon Regions
Known Junctions

Normalized expression data for each known or novel expressed feature of 'CDCA3'

The following table summarizes the expression values of all known features of the gene 'CDCA3' in each library. Known features (i.e. those that correspond to one or more EnsEMBL transcripts) are included regardless of their expression level. Novel features are only reported in this table if they are expressed above the level of intergenic background noise. The 'FID' column reports the unique Feature ID for the gene, transcript, exon region, exon junction, etc. The 'Name' column reports the Feature Name for the feature (e.g. E5a_E6a is the name of an exon junction corresponding to the connection of exons 5 and 6). The 'Type' column reports the type of the feature and may be one of the following: Gene, Transcript, Exon Region, Known Junction, Novel Junction, Known Boundary, Novel Boundary, Silent or Active Intronic Regions, and Silent or Active Intergenic Regions (see our manuscript for more details). The 'Base Count' column reports the number of nucleotide bases for the feature followed by the percent of these that do NOT correspond to repeats and the percent that are known to be protein coding in one or more EnsEMBL transcripts. The 'Supporting ESTs/mRNAs' column reports the number of ESTs and mRNAs that when aligned to the human genome support the expression of a feature (i.e. the sequence alignment coordinates match an exon junction or boundaries of an exon, retained intron, etc.). The 'Conserved Species' column reports the number of 'other' species for which there was at least 1 supporting EST/mRNA alignment. Finally, the remaining columns report the log2 expression value for each feature in each library. Bold values indicate expression above background. Each expression value is also a hyperlink to a view of the feature's corresponding genomic region in the UCSC genome browser. Expression data will automatically be loaded as custom GFF and wiggle tracks.

FIDNameTypeBase Count
(% unmasked |
% coding)
SUM149_DMSO Log2
SUM149_IR Log2
A431_DMSO Log2
A431_IR Log2
PC9_IR Log2
G4000CDCA3Gene1110 (100% | 73%)N/AN/A7.93 (C | P)7.15 (C | P)7.15 (C | P)6.28 (C | P)6.76 (C | P)6.65 (C | P)
T10271ENST00000229265Transcript1420 (100% | 74%)N/AN/A8.18 (C | P)7.45 (C | P)7.38 (C | P)6.30 (C | P)7.11 (C | P)7.00 (C | P)
ER33005ER1aExonRegion40 (100% | 0%)048.53 (C | P)7.95 (C | P)7.35 (C | P)5.86 (C | P)7.86 (C | P)8.19 (C | P)
EJ580616E1a_E2aKnownJunction62 (100% | 0%)3608.25 (C | P)7.94 (C | P)7.60 (C | P)5.75 (C | P)7.90 (C | P)7.24 (C | P)
ER33006ER2aExonRegion177 (100% | 68%)3317.52 (C | P)6.63 (C | P)6.69 (C | P)5.69 (C | P)6.71 (C | P)7.12 (C | P)
EJ580621E2a_E3aKnownJunction62 (100% | 100%)4008.65 (C | P)7.92 (C | P)7.34 (C | P)6.76 (C | P)7.69 (C | P)7.81 (C | P)
ER33007ER3aExonRegion130 (100% | 100%)4028.24 (C | P)7.40 (C | P)7.23 (C | P)6.37 (C | P)6.48 (C | P)6.83 (C | P)
EJ580625E3a_E4aKnownJunction62 (100% | 100%)4008.05 (C | P)6.74 (C | P)7.49 (C | P)6.24 (C | P)6.24 (C | P)5.83 (C | P)
ER33008ER4aExonRegion294 (100% | 100%)1178.08 (C | P)7.47 (C | P)7.51 (C | P)6.60 (C | P)7.17 (C | P)6.58 (C | P)
EJ580628E4a_E5aKnownJunction62 (100% | 100%)1208.24 (C | P)7.41 (C | P)7.58 (C | P)6.47 (C | P)6.78 (C | P)5.46 (C | P)
EJ580629E4a_E6aNovelJunction62 (100% | 100%)102.97 (C | P)3.75 (C | P)3.46 (C | P)0.00 (C | P)5.60 (C | P)0.00 (C | P)
ER33009ER5aExonRegion107 (100% | 100%)1018.21 (C | P)7.55 (C | P)7.28 (C | P)6.55 (C | P)6.82 (C | P)6.75 (C | P)
EJ580630E5a_E6aKnownJunction62 (100% | 100%)1408.15 (C | P)7.53 (C | P)7.82 (C | P)6.47 (C | P)7.08 (C | P)7.04 (C | P)
ER33010ER6aExonRegion362 (100% | 43%)707.67 (C | P)6.66 (C | P)6.91 (C | P)6.15 (C | P)6.18 (C | P)5.82 (C | P)
IG3550IG31Intergenic1443 (25% | 0%)004.14 (C | P)3.50 (C | P)1.49 (C | P)0.84 (C | P)1.14 (C | P)1.79 (C | P)
AIG15291IG31_AR3ActiveIntergenicRegion28 (100% | 0%)205.71 (C | P)4.68 (C | P)0.50 (C | P)2.98 (C | P)0.00 (C | P)3.04 (C | P)
AIG15290IG31_AR2ActiveIntergenicRegion746 (4% | 0%)205.50 (C | P)4.28 (C | P)2.20 (C | P)1.72 (C | P)0.00 (C | P)1.84 (C | P)
SIG13468IG31_SR1SilentIntergenicRegion660 (44% | 0%)003.50 (C | P)3.20 (C | P)1.48 (C | P)0.00 (C | P)1.32 (C | P)1.61 (C | P)

Figures displaying gene and feature expression levels in each library

The following figures illustrate the expression of the gene 'CDCA3' and its component features for each library. First the expression values are displayed for only the exons and known (or expressed novel) exon junctions. This first display consists of a single plot with one colored line per library (as indicated in the legend). Next, the expression of the gene relative to the distribution of all gene expression values is displayed as a histogram. In these figures (one for each library) the expression of the current gene is indicated by a dotted red line. Estimated cutoffs for background expression level corresponding to intergenic and intragenic noise are indicated by dotted black lines. The bar plots following these histograms display the expression level of all individual features. The color of the bars correspond to different feature types (enumerated as colored boxes in the legend). As in the histograms, the estimated cutoffs level for intergenic and intragenic noise are indicated as dotted lines. For genes with low expression values, these cutoffs converge to a single value. *If you can not see the figure below, click here