MmuEX0048668 @ mm9
Exon Skipping
Gene
ENSMUSG00000029817 | Tra2a
Description
transformer 2 alpha homolog (Drosophila) [Source:MGI Symbol;Acc:MGI:1933972]
Coordinates
chr6:49202381-49214051:-
Coord C1 exon
chr6:49213837-49214051
Coord A exon
chr6:49202807-49203107
Coord C2 exon
chr6:49202381-49202514
Length
301 bp
Sequences
Splice sites
3' ss Seq
AATGTTCTTTTTCCATTAAGGTT
3' ss Score
8.88
5' ss Seq
TAGGTTAAG
5' ss Score
-0.45
Exon sequences
Seq C1 exon
GGTTTCTGGCGGCACGGGCGCCATTTTGCCTGAACGTGCGAGCTGGTGGGAGTGGAACGCACTGGCCGTTGTAGCCGTCGCCTTCTTCCTCCCCACAGTCCGAACAGCGCGGTGACTAGGCCGTCGGCCCTCGAGCCGAGACATATCTCTTATTTAGTTCTCGGGAGCGCCTGGCCGACATGAGTGATGTAGAGGAGAACAACTTCGAGGGCAGA
Seq A exon
GTTAATGTTCGTGAAGAAATTGAAGAGTTTTTTCCAAGAATGTGGAAGATAAATCAAGATAAAAGAAGGCTAATGAAAAGTATTAAAGATCAGAAAATTAAAATTGAATGGGGGAAAAAATTGAACAGAAGATTGGTCAGATAGAAGCACTTGAATATTTTTTTAAGGCTATTTTGAATTGTTTGAATTGGGGAAGAATACACGAAGTATGAAAAATGAAAAACTCAATGAAGAATGAAGAGAAGTAGAAAGCAAGAGTGAAGTAGAATTAAAAGAATCTGGAAGAATGAATGGGTCCTAG
Seq C2 exon
GAGTCTCGCTCTCAGTCAAAATCTCCAACGGGAACTCCTGCTCGTGTAAAATCAGAGAGCAGGTCAGGATCTCGTAGTCCATCACGGGTGTCCAAACATTCTGAATCCCATTCTCGATCAAGATCAAAGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029817_MULTIEX1-1/2=C1-2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.700 A=0.000 C2=1.000
Domain overlap (PFAM):
C1:
PF104084=Ufd2P_core=PU(20.0=83.3)
A:
PF104084=Ufd2P_core=PD(76.0=79.2)
C2:
PF086487=DUF1777=FE(33.6=100)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATTTTGCCTGAACGTGCGAG
R:
CTGGACTTTGATCTTGATCGAGA
Band lengths:
328-629
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]
SPECIAL DATASETS
- Pre-implantation embryo development
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: