HsaEX0027034 @ hg19
Exon Skipping
Gene
ENSG00000136895 | GARNL3
Description
GTPase activating Rap/RanGAP domain-like 3 [Source:HGNC Symbol;Acc:25425]
Coordinates
chr9:130007616-130053521:+
Coord C1 exon
chr9:130007616-130007699
Coord A exon
chr9:130027231-130027300
Coord C2 exon
chr9:130053447-130053521
Length
70 bp
Sequences
Splice sites
3' ss Seq
ATGAAGCATTTTTGTTCCAGCTC
3' ss Score
4.98
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
Exon sequences
Seq C1 exon
GATTGGCGGCCGGAGGGATGGCAAAGCTGCCACGCGCACGGGGGTGCAGGCTGCGGGACTGCGATCGCTGCCGGATAGGACCAG
Seq A exon
CTCTGTCTCGGAAGACCTAGGCTGTAGACGTGGGGATTTCAGTAGGAAACATTATGGATCTGTGGAGCTG
Seq C2 exon
CTTATTTCCAGTGATGCTGATGGAGCCATCCAAAGGGCTGGAAGATTCAGAGTGGAAAATGGCTCTTCAGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136895-'8-19,'8-17,12-19
Average complexity
C2
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (Iupred):
C1=NA A=0.000 C2=0.229
Domain overlap (PFAM):
C1:
NA
A:
NO
C2:
NO
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAGGGATGGCAAAGCTG
R:
TGAAGAGCCATTTTCCACTCTGA
Band lengths:
143-213
Functional annotations
There are 1 annotated functions for this event
PMID: 31911676
This event
[CRISPR screen]. Conserved poison exon with negative fitness/survivability impact when depleted: HeLa Depleted at 14 days (FC=0.774, FDR=0.001), PC9 No Change at 14 days (FC=1.238, FDR=0.436), Late Xenograft No change (FC=0.852, FDR=0.023).
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)