BtaEX0035380 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000020975 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497]
Coordinates
chr23:7562403-7566784:+
Coord C1 exon
chr23:7562403-7562493
Coord A exon
chr23:7563353-7563432
Coord C2 exon
chr23:7566088-7566784
Length
80 bp
Sequences
Splice sites
3' ss Seq
CCCACTCTCTCCCCCTGCAGCTC
3' ss Score
12.54
5' ss Seq
CAGGTTGGT
5' ss Score
8.08
Exon sequences
Seq C1 exon
GCTGATGCTGGTGGAGGAGGAGCTGCGCCGGGACCACCCCACCATGGCTGAGCCGCTGCCCGAACCCAAGAAGAGGCTGCTCGACGCTCAG
Seq A exon
CTCCTCATCAGGTAATTCTCCTGGTTCCGCTTTGACCACGGGCGGAGGACACAGGGGGAGGTGACTCCGGACCACTACAG
Seq C2 exon
GAGAGGCAGCTTCCCCCCTTGGGTCCAACAAACCCGCGTGTGACGCTGGCCCCACCTTGGAACGGCCTGGCCCCCCCAGCCCCACCTCCCCCACCCCGGCTGCAGATCACTGAGAACGGCGAGTTCCGAAACACCGCAGACCACTAGCCCACCCAGCATCTCAGACCTCCTCCTCCCTCCCTGTGCACCCCACCCTGGAACGGCACCAACCACCAGGACTGGACGTCGCCGAGGGACAGCGGGATCGCCTCCTTGAACGCCTCCTTGCGGGGCACCAGTCCCCCACCCCCACTGCACCATTTCTGGGAGGGAGAGCGGGGACCCTCAGCTGCCCCCTTTTCCTTCCTGCTGGGGTGCTGTCCCCTGTGACCCCAAGGACCCTTGCCCCAGGACACAGACCCCTTCACTCCGGGGTGCTATCCCCATCCTCTGCCTCATCGTTCCCCTGAGCACTGGGGGACAGACCCTCACCCCCACCCTGGGGGTGCGGCACCTCCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020975_MULTIEX2-1/2=C1-C2
Average complexity
S*
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=0.000 C2=1.000
Domain overlap (PFAM):
C1:
PF120043=DUF3498=FE(5.0=100)
A:
PF120043=DUF3498=PD(0.2=20.0)
C2:
PF120043=DUF3498=PD(2.8=34.7)
Main Inclusion Isoform:
ENSBTAT00000027936fB6886
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACCCAAGAAGAGGCTGCTC
R:
CTAGTGGTCTGCGGTGTTTCG
Band lengths:
177-257
Functional annotations
There are 1 annotated functions for this event
PMID: 31911676
[CRISPR screen]. Conserved poison exon with pro-oncogenic impact when depleted: HeLa No Change at 14 days (FC=0.831, FDR=0.036), PC9 No Change at 14 days (FC=0.883, FDR=0.319), Late Xenograft Enriched (FC=1.949, FDR=0.000).
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development