GgaEX0016438 @ galGal4
Exon Skipping
Gene
ENSGALG00000010973 | TRA2A
Description
transformer-2 protein homolog alpha [Source:RefSeq peptide;Acc:NP_001006360]
Coordinates
chr2:31428358-31437334:-
Coord C1 exon
chr2:31437114-31437334
Coord A exon
chr2:31429076-31429081
Coord C2 exon
chr2:31428358-31428491
Length
6 bp
Sequences
Splice sites
3' ss Seq
AATGTTCTTTTTCCATTAAGGTT
3' ss Score
8.88
5' ss Seq
AATGTTCGT
5' ss Score
-3.71
Exon sequences
Seq C1 exon
GAAGCGGAGGCGCCATTTTGCGCTGCTGCGGGAGACGGGTTGGGAGGCTTTGGCGGGAGGGAGGCGGCGGTGGCGGTAGGGATAGCATTAACCGCGGTAACCATAGCGGTAGCGGCGGTGGGTGCGGTCGCTGCTCGGGACTAGCGTCCCCGTTCGCCCGGCCCCGCGGTCAGGACTTTGCCGACATGAGCGACGTGGAGGAGAACAACTTCGAGGGGAGG
Seq A exon
GTTAAT
Seq C2 exon
GAGTCTCGCTCCCAGTCAAAATCTCCAGCTGGGAGTCCTGCTCGTGTAAAATCGGAGAGCAGGTCAGGATCTCGCAGTCCATCGAGAGCTTCCAAACATTCTGAATCACACTCTAGGTCAAGATCAAAATCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010973-MICROEX1
Average complexity
MIC-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
Show structural model
Features
Disorder rate (Iupred):
C1=0.750 A=1.000 C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
NO
Main Inclusion Isoform:
ENSGALT00000017877fB1918
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:
GTCAGGACTTTGCCGACATGA
R:
TTTACACGAGCAGGACTCCCA
Band lengths:
103-109
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]