RnoEX0070102 @ rn6
Exon Skipping
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38727903-38740020:-
Coord C1 exon
chr3:38739889-38740020
Coord A exon
chr3:38738379-38738458
Coord C2 exon
chr3:38727903-38727983
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
ATGGGGCATCCTGGCATGCATTATGCACCAATGGGCATGCACCCTATGGGTCAGCGAGCAAACATGCCTCCTGTACCTCACGGAATGATGCCACAGATGATGCCTCCTATGGGAGGGCCTCCAATGGGACAA
Seq A exon
AAAGATAAAATAAAACAATTTGCTACTGCCAGATGCTTCTTTCTTTTCTGGGGCCTTCTGTTTCCATTGGGCCAGTCAAG
Seq C2 exon
ATGCCTGGAATGATGTCTTCAGTAATGTCAGGAATGATGATGTCTCATATGTCTCAGGCTTCCATGCAACCTGCTTTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864-'4-3,'4-2,5-3
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.991 A=0.111 C2=0.866
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
NO
Main Inclusion Isoform:
ENSRNOT00000006549fB11420
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:
TTATGCACCAATGGGCATGCA
R:
GTTGCATGGAAGCCTGAGACA
Band lengths:
182-262
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]