DreEX0080931 @ danRer10
Exon Skipping
Gene
ENSDARG00000007863 | tra2a
Description
transformer 2 alpha homolog (Drosophila) [Source:ZFIN;Acc:ZDB-GENE-040426-1391]
Coordinates
chr19:20593564-20595119:+
Coord C1 exon
chr19:20593564-20593737
Coord A exon
chr19:20594331-20594654
Coord C2 exon
chr19:20594986-20595119
Length
324 bp
Sequences
Splice sites
3' ss Seq
AATGTTCTTTTTTCATTAAGGTT
3' ss Score
8.31
5' ss Seq
TAAGTAAAT
5' ss Score
1.48
Exon sequences
Seq C1 exon
GATTCGCCTCCCACAGTACACCGCGCGTTTCAGATGGTCGGCCATTTTCTGCAGTTACATTAGGAGCGGAAGTCTTCGTCGAAGAGCGTCTTCATATCCACGCTTTTTTTTTTACCAGTCAATAATATTTTTAAAACAATGAGTGATACTGAAGAGCAACAATTCCAGAGGAGG
Seq A exon
GTTATTGGTCGTGAAGGATTTGAAGAGTTAAGGCCAAGAATGTGGAAGAATATTCAAGATAAAAGAAGGCTTTTACAGAGAAAATGTTTACAGAGCAGACGGTTAAGTGGGAAGGGGAAAAAAGAACGGAAGATCGGTCAGATAGAAGCACGCTTGCGTTATGTGTCTAAAGCAGAAAAAAGAAAAGAGGTTTCAGATTGGGGTGAAGAAATGAAAAGGAGAGGAAAAATGAAAACTGAACAAATGAAGACCGAAGAATAAAATGCCTGAAAGAAAGGAATAGCGTATACTGAAAACAGAAGAATGAATGAGTCCGTAGGCTAA
Seq C2 exon
GAATCTCGCTCGGCGTCCAAATCGGATCGGGGGAGTCCTGCCCAACCCAAGATGGAGAGCAGGTCTGGTTCTCCCAGCCCTTCCAGAGCATCCAAGCGTTCTGATTCAAGATCAAGATCACGCTCCAAGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000007863_CASSETTE1
Average complexity
S*
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.954 A=0.453 C2=1.000
Domain overlap (PFAM):
C1:
PF086487=DUF1777=PU(6.5=83.3)
A:
NO
C2:
PF086487=DUF1777=PU(21.8=96.4)
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATTCGCCTCCCACAGTACAC
R:
TGGACTTGGAGCGTGATCTTG
Band lengths:
307-631
Functional annotations
There are 3 annotated functions for this event
PMID: 30916337
Experimentally validated NMD (response to KD of NMD machinery; from 18443041) and eCLIP binding in an autoregulatory loop.
PMID: 31911676
[CRISPR screen]. Conserved poison exon with mixed impact when depleted: HeLa Enriched at 14 days (FC=1.256, FDR=0.002), PC9 No Change at 14 days (FC=1.256, FDR=0.158), Late Xenograft Depleted (FC=0.604, FDR=0.000).
PMID: 33176162
Poison exons in serine-arginine-rich (SR) proteins, a family of 14 essential SFs, are differentially spliced during induced pluripotent stem cell (iPSC) differentiation and in tumors versus normal tissues. The study uncovers an extensive cross-regulatory network of SR proteins controlling their expression via alternative splicing coupled to nonsense-mediated decay. This TRA2A PE is in the CDS.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]