HsaEX0026818 @ hg19
Exon Skipping
Gene
ENSG00000128683 | GAD1
Description
glutamate decarboxylase 1 (brain, 67kDa) [Source:HGNC Symbol;Acc:4092]
Coordinates
chr2:171704186-171705860:+
Coord C1 exon
chr2:171704186-171704302
Coord A exon
chr2:171705193-171705304
Coord C2 exon
chr2:171705796-171705860
Length
112 bp
Sequences
Splice sites
3' ss Seq
CTCTCTGCCCATTTTCTTAGGGA
3' ss Score
9.54
5' ss Seq
ATGGTACCC
5' ss Score
4.36
Exon sequences
Seq C1 exon
GGATATGTTCCCTTTTATGTCAATGCAACTGCTGGCACGACTGTTTATGGAGCTTTTGATCCGATACAAGAGATTGCAGATATATGTGAGAAATATAACCTTTGGTTGCATGTCGAT
Seq A exon
GGATTTAACTTCTCACAATTGGCCAATAGGATCATCTGCCTTGCTACTGAACTAATGACTAACAAAGGCTGTGTCACGTGGCATCCCAACTATTCAGTAAACATGCATCATG
Seq C2 exon
GCTGCCTGGGGAGGTGGGCTGCTCATGTCCAGGAAGCACCGCCATAAACTCAACGGCATAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128683_MULTIEX2-2/2=1-C2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
In the CDS, with uncertain impact
Show PDB structure
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0028214=Pyridoxal_deC=FE(10.1=100)
A:
PF0028214=Pyridoxal_deC=PD(0.4=2.6)
C2:
PF0028214=Pyridoxal_deC=FE(5.6=100)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
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:
ATGTTCCCTTTTATGTCAATGCAACT
R:
CTTTCTATGCCGTTGAGTTTATGGC
Band lengths:
178-290
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 No Change at 14 days (FC=1.012, FDR=0.905), PC9 No Change at 14 days (FC=0.806, FDR=0.024), Late Xenograft Depleted (FC=0.776, FDR=0.009).
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)