HsaEX0055439 @ hg19
Exon Skipping
Gene
ENSG00000005175 | RPAP3
Description
RNA polymerase II associated protein 3 [Source:HGNC Symbol;Acc:26151]
Coordinates
chr12:48063890-48073557:-
Coord C1 exon
chr12:48073487-48073557
Coord A exon
chr12:48073276-48073377
Coord C2 exon
chr12:48063890-48064128
Length
102 bp
Sequences
Splice sites
3' ss Seq
GTTATAAATTTATTTTCAAGGAA
3' ss Score
6.45
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
Exon sequences
Seq C1 exon
ATTTTGAAACTGTTTTACTTCTGGAACCTGGAAATAAGCAAGCAGTAACTGAACTCTCCAAAATTAAAAAG
Seq A exon
GAATTAATTGAGAAAGGACACTGGGATGATGTCTTTCTTGATTCCACACAAAGACAAAATGTGGTAAAACCCATTGATAATCCACCGCATCCTGGATCAACT
Seq C2 exon
AAACCACTCAAGAAGGTTATTATTGAAGAAACTGGTAATTTGATACAGACTATTGATGTGCCAGATAGCACTACTGCTGCTGCTCCAGAGAATAATCCTATTAATCTAGCAAATGTAATAGCAGCCACAGGCACCACAAGTAAGAAGAATTCAAGCCAAGATGACCTTTTTCCCACAAGTGATACTCCAAGAGCAAAAGTATTGAAAATAGAAGAAGTCAGTGATACTTCATCCCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000005175_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
Show structural model
Features
Disorder rate (Iupred):
C1=0.010 A=0.471 C2=0.694
Domain overlap (PFAM):
C1:
PF0051523=TPR_1=PD(32.4=45.8)
A:
NO
C2:
NO
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAACCTGGAAATAAGCAAGCA
R:
GCTCTTGGAGTATCACTTGTGGG
Band lengths:
244-346
Functional annotations
There are 1 annotated functions for this event
PMID: 23159623
This event
The exon is required for the protein's interaction with PIH1D1, which protects the cell against apoptosis. Knockdown of the isoform containing the exon down-regulates PIH1D1 protein level, without affecting mRNA level, suggesting the inclusion isoform stabilizes the R2AP3 protein complex (involved in cell survival) of which they both belong, whereas the skipping isoform has a dominant negative effect on the R2TP complex.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)