DreEX0080935 @ danRer10
Exon Skipping
Gene
ENSDARG00000002168 | tra2b
Description
transformer 2 beta homolog (Drosophila) [Source:ZFIN;Acc:ZDB-GENE-040426-1094]
Coordinates
chr9:12618736-12623556:-
Coord C1 exon
chr9:12623383-12623556
Coord A exon
chr9:12619219-12619478
Coord C2 exon
chr9:12618736-12618881
Length
260 bp
Sequences
Splice sites
3' ss Seq
TCCTTTTCTTTTTTGTTAAGGTT
3' ss Score
9.19
5' ss Seq
TTAGTATGT
5' ss Score
2.85
Exon sequences
Seq C1 exon
TTCTAAATAAAGCTTCTACGGCGAGAAAGGCGTTCATTTACAGACGTCTGGTTTGTGTGTGCGTTTGAGCACTACTTGTGTGTTGTCCTAATCATTTCTCTTGCATTGTAATTATTGCAGCATATTACAAACTAAACAAAAATGAGTGACGCCGAGAAGGAATTCGTGGAGCGG
Seq A exon
GTTAAGGTTGGAAGAAGAGAAATCTGGATGAAGTCAAATGTCAAGTTGTTAATGCGAATAATTTGAAGCTGAATTTTCAGTGCATGCTAATATTGCGGAGCAAAAGAAGTTCCCATATAGCATTTTTGGGCAGTGAGAGAAATGGGGGAAGAGGATTGAAGTCAGAAATGAAATTGAGACTGAAGAAAGAAGAAAAGATGTGTTATGAAGTTAAGATCAGAAGTTATCTGGGATAAGATCGCAGCGCTAAGTAACTCTTA
Seq C2 exon
GAGTCTCGTTCAGCCTCTAGGAGCGCAAGTCCTAGAGGATCTGCCAAGTCCGGCAGTCGCTCAGCTGAACGCTCGCCTGCTCATTCCAAAGAGAGGTCCCATCATTCCCGCTCAAAATCCCGCTCGCGCTCCCGTTCCAAGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002168-'0-3,'0-1,3-3=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=0.000 C2=1.000
Domain overlap (PFAM):
C1:
PF131361=DUF3984=PU(10.8=90.9),PF086487=DUF1777=PU(8.2=81.8),PF072186=RAP1=PU(8.1=72.7)
A:
PF044847=DUF566=FE(0.5=100)
C2:
PF131361=DUF3984=FE(51.6=100),PF086487=DUF1777=FE(43.6=100),PF072186=RAP1=FE(48.5=100)
Main Inclusion Isoform:
ENSDART00000021266fB6781
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGCTTCTACGGCGAGAAAGG
R:
GTCTTGGAACGGGAGCGC
Band lengths:
308-568
Functional annotations
There are 4 annotated functions for this event
PMID: 14709600
TRA2-BETA1 (canonical isoform) binds to four enhancers present in exon 2 HsaEX0066781), which activates its inclusion. Inclusion of exon 2 generates mRNAs that are not translated into proteins. HTRA2-BETA1 interacting proteins promote exon 2 skipping by sequestering it, which upregulates the HTRA2-BETA1 protein synthesis. It is proposed that the regulation of the tra2-beta pre-mRNA alternative splicing provides a robust and sensitive molecular sensor that measures the ratio between HTRA2-BETA1 and its interacting proteins.
PMID: 31911676
[CRISPR screen]. Conserved poison exon with mixed impact when depleted: HeLa Enriched at 14 days (FC=1.571, FDR=0.000), PC9 No Change at 14 days (FC=0.954, FDR=0.648), Late Xenograft Depleted (FC=0.512, 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.
PMID: 33176162
Splice-switching antisense oligonucleotides that reverse the increased skipping of TRA2B-Poison exon detected in breast tumors, alters breast cancer cell viability, proliferation, and migration.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]