HsaEX0027035 @ hg19
Exon Skipping
Gene
ENSG00000136895 | GARNL3
Description
GTPase activating Rap/RanGAP domain-like 3 [Source:HGNC Symbol;Acc:25425]
Coordinates
chr9:130117576-130119656:+
Coord C1 exon
chr9:130117576-130117751
Coord A exon
chr9:130118708-130118784
Coord C2 exon
chr9:130119498-130119656
Length
77 bp
Sequences
Splice sites
3' ss Seq
CCATCTCTTATCTTTTAAAGACT
3' ss Score
5.97
5' ss Seq
AAGGTATTT
5' ss Score
7.64
Exon sequences
Seq C1 exon
GCTGCCACCTGTATGCTATTAACACTCACCACAGCAGAGAGCTGAGGATTGTGGTTGCAATTCGGAATAAACTGCTTCTGATCACAAGAAAACACAACAAGCCAAGCGGGGTCACCAGCACCTCATTGTTATCTCCCCTGTCTGAGTCACCTGTTGAAGAATTCCAGTACATCAGG
Seq A exon
ACTAGGGTACATTAAGGTATGGAATATATCTAGCATTGGCCACTAAGATGGAGTATTTCTACTGGAGAGCTGAGAAG
Seq C2 exon
GAGATCTGTCTGTCTGACTCTCCCATGGTGATGACCTTAGTGGATGGGCCAGCTGAAGAGAGTGACAATCTCATCTGTGTGGCTTATCGACACCAATTTGATGTGGTGAATGAGAGCACAGGAGAAGCCTTCAGGCTGCACCACGTGGAGGCCAACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136895_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.073 A=0.000 C2=0.009
Domain overlap (PFAM):
C1:
PF0078017=CNH=FE(19.0=100)
A:
PF0078017=CNH=PD(0.1=0.0)
C2:
PF0078017=CNH=FE(17.0=100)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
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:
ATCTCCCCTGTCTGAGTCACC
R:
AGGCTTCTCCTGTGCTCTCAT
Band lengths:
176-253
Functional annotations
There are 1 annotated functions for this event
PMID: 31911676
This event
[CRISPR screen]. Non-conserved poison exon with negative fitness/survivability impact when depleted: HeLa Depleted at 14 days (FC=0.612, FDR=0.000), PC9 No Change at 14 days (FC=0.967, FDR=0.767), Late Xenograft No change (FC=0.947, FDR=0.309).
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)