HsaEX0066781 @ hg38
Exon Skipping
Gene
ENSG00000136527 | TRA2B
Description
transformer 2 beta homolog (Drosophila) [Source:HGNC Symbol;Acc:HGNC:10781]
Coordinates
chr3:185926601-185938136:-
Coord C1 exon
chr3:185937825-185938136
Coord A exon
chr3:185931577-185931852
Coord C2 exon
chr3:185926601-185926734
Length
276 bp
Sequences
Splice sites
3' ss Seq
CCTGTTCTTTTTCTATTAAGGTT
3' ss Score
10.29
5' ss Seq
TAAGTAATT
5' ss Score
1.76
Exon sequences
Seq C1 exon
GTGCGGGACGCGCTGCAGCTGGAGAGGAAAGGCAGAGCGAGGAGGGGCGAGGCCAAGAAAGCGCGCGTTTCTGGGAGGGGAGGAGCCTGGCTAAGGAGCGCCGCGTCACATCCGGTAGAGTTAGAGCCCGTGCGGAGGCGGTGCGGAGCATTTCGGCTCTGAGCGGCTGGGCGACCGGCGCGTCGTGCGGGGCTGCGGCGGAGCCTCCTTAAGGAAGGTGCAAGAGGTTGGCAGCTTCGATTGAAGCACATCGACCGGCGACAGCAGCCAGGAGTCATGAGCGACAGCGGCGAGCAGAACTACGGCGAGCGG
Seq A exon
GTTAATGTTGAAGAAGGAAAATGCGGAAGTCGTCATTTGACAAGTTTTATAAATGAGTATTTGAAGCTCAGGAATAAGTGAAGCTGAAATTTGAAAAAATAAAAGAAAGAATGCATGCTAATTATCAGACCAGAAGTCCCACTTGTAGAATATTGAGCAATTTGTGTGAAGTGGGGAAGATGAAAGAAGTCAGAATTTGAAACGGAAGAATGAAGAAAAGAAATAAAAATGAAGTTAAGATAAGAAGTAATCTGGAATCAGAAAGCACTACGCTAA
Seq C2 exon
GAATCCCGTTCTGCTTCCAGAAGTGGAAGTGCTCACGGATCGGGGAAATCTGCAAGGCATACCCCTGCAAGGTCTCGCTCCAAGGAAGATTCCAGGCGTTCCAGATCAAAGTCCAGGTCCCGATCTGAATCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136527_MULTIEX2-2/4=C1-4
Average complexity
C1*
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.917 A=0.281 C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
NO
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCCGGTAGAGTTAGAGCCCG
R:
TCTTCCTTGGAGCGAGACCTT
Band lengths:
292-568
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]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development