GgaEX0016438 @ galGal3
Exon Skipping
Gene
ENSGALG00000010973 | TRA2A
Description
NA
Coordinates
chr2:31223183-31232023:-
Coord C1 exon
chr2:31231945-31232023
Coord A exon
chr2:31223595-31223906
Coord C2 exon
chr2:31223183-31223316
Length
312 bp
Sequences
Splice sites
3' ss Seq
AATGTTCTTTTTCCATTAAGGTT
3' ss Score
8.88
5' ss Seq
AATGTATGG
5' ss Score
3.37
Exon sequences
Seq C1 exon
GCGTCCCCGTTCGCCCGGCCCCGCGGTCAGGACTTTGCCGACATGAGCGACGTGGAGGAGAACAACTTCGAGGGGGAGG
Seq A exon
GTTAATGTTCGTGAAGAAATTGAAGAGTTTTTTCCAAGAATGTGGAAGATAAATCAAGATAAAAGAAGGCTAATGAAAAGTATTAAAGATCAGAAAAATAAAATTGAATGGGGGAAAAAATTGAACAGAAGATTGGTCAGATAGAAGCACTTGAATGTTTTTTTAAGGCTATAATGAATTGTTTGAATTGGGGAAGAATACACGAAGTATGAAAAATGAAAAACTCAATGAAGAATGAAGAAAAGTAGAAAGCAAGAGTGAAGTAGAATTAAAAGAATCTGGAAGAATGAATGGGTCCTAGGTTAAGTAAAT
Seq C2 exon
GAGTCTCGCTCCCAGTCAAAATCTCCAGCTGGGAGTCCTGCTCGTGTAAAATCGGAGAGCAGGTCAGGATCTCGCAGTCCATCGAGAGCTTCCAAACATTCTGAATCACACTCTAGGTCAAGATCAAAATCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010973-'1-3,'1-2,4-3
Average complexity
C1
Mappability confidence:
86%=67=100%
Protein Impact
ORF disruption upon sequence inclusion
Show structural model
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
NO
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGTCAGGACTTTGCCGACAT
R:
CTCGATTTTGATCTTGACCTAGAGTG
Band lengths:
190-502
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.