HsaEX0050372 @ hg38
Exon Skipping
Gene
ENSG00000196504 | PRPF40A
Description
pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr2:152694542-152716126:-
Coord C1 exon
chr2:152715995-152716126
Coord A exon
chr2:152714550-152714629
Coord C2 exon
chr2:152694542-152694622
Length
80 bp
Sequences
Splice sites
3' ss Seq
AAATTAGTTTCTTTCCACAGAAA
3' ss Score
7.37
5' ss Seq
AAGGTAAGT
5' ss Score
11
Exon sequences
Seq C1 exon
ATGGGGCACCCTGGCATGCATTATGCCCCAATGGGAATGCACCCTATGGGTCAGAGAGCGAATATGCCTCCTGTACCTCATGGAATGATGCCGCAGATGATGCCCCCTATGGGAGGGCCACCAATGGGACAA
Seq A exon
AAAGATAAAATAAAACAATTTGCTACTGCCAGATGCTTCTCTCTTTTCTGGGGCCTTCTGTTTCCATTGGGCCAATCAAG
Seq C2 exon
ATGCCTGGAATGATGTCGTCAGTAATGCCTGGAATGATGATGTCTCATATGTCTCAGGCTTCCATGCAGCCTGCCTTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504_MULTIEX1-2/8=1-4
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.901 A=0.185 C2=0.831
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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:
GGCACCCTGGCATGCATTAT
R:
TGAGACATCATCATTCCAGGCA
Band lengths:
175-255
Functional annotations
There are 1 annotated functions for this event
PMID: 31911676
[CRISPR screen]. Conserved poison exon with mixed impact when depleted: HeLa Enriched at 14 days (FC=1.375, FDR=0.000), PC9 No Change at 14 days (FC=1.346, FDR=0.041), Late Xenograft Depleted (FC=0.722, FDR=0.001).
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