RnoEX0093154 @ rn6
Exon Skipping
Gene
ENSRNOG00000009156 | Tra2a
Description
transformer 2 alpha homolog [Source:RGD Symbol;Acc:1562563]
Coordinates
chr4:78913333-78924181:-
Coord C1 exon
chr4:78923982-78924181
Coord A exon
chr4:78913748-78914060
Coord C2 exon
chr4:78913333-78913466
Length
313 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
CCGGCGCCATTTTGCCCGAGCGTGCGAGCTAGTGGGAGTGGAACGCACCGGCCGTTGTAGCCGTCGCCTTCTTCCTCCCCACAGTCAAACAGCGCGGTGACTAGGCCGTCGGCCCTCGAGCCGAGACATATCTCTTGTTTAGTGCTCGGGAGCGCCTGGCCAACATGAGTGATGTAGAGGAGAACAACTTCGAGGGCAGA
Seq A exon
GTTAATGTTCGTGAAGAAATTGAAGAGTTTTTTCCAAGAATGTGGAAGATAAATCAAGATAAAAGAAGGCTAATGAAAAGTATTAAAGATCAGAAAATTAAAATTGAATGGGGGAAAAAATTGAACAGAAGATTGGTCAGATAGAAGCACTTGAATATTTTTTTTAAGGCTATTTTGAATTGTTTGAATTGGGGAAGAATACACGAAGTATGAAAAATGAAAAACTCAATGAAGAATGAAGAGAAGTAGAAAGCAAGAGTGAAGTAGAATTAAAAGAATCTGGAAGAATGAATGGGTCCTAGGTTAAGTAAAT
Seq C2 exon
GAGTCTCGCTCTCAGTCAAAATCTCCAACGGGAACTCCTGCTCGTGTAAAATCAGAGAGCAGGTCAGGATCTCGTAGTCCATCAAGGGTTTCCAAACATTCTGAATCCCATTCTCGATCAAGATCAAAATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009156_MULTIEX2-3/3=C1-C2
Average complexity
ME(1-3[99=100])
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.600 A=0.000 C2=0.844
Domain overlap (PFAM):
C1:
PF104084=Ufd2P_core=PU(20.0=83.3)
A:
PF104084=Ufd2P_core=PD(76.0=79.2)
C2:
PF0345912=TOBE=PD(31.7=50.0)
Main Inclusion Isoform:
ENSRNOT00000012325fB15535
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCATTTTGCCCGAGCGT
R:
GGATTTTGATCTTGATCGAGAATGGG
Band lengths:
327-640
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]