BtaINT0118366 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016589 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:25031]
Coordinates
chr5:30373960-30374446:-
Coord C1 exon
chr5:30374269-30374446
Coord A exon
chr5:30374022-30374268
Coord C2 exon
chr5:30373960-30374021
Length
247 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
GGGAATTTTTCCATCTCCAGATC
3' ss Score
7.9
Exon sequences
Seq C1 exon
GGCTCTGAGTCAGGAGATGAGGAGCTGCCCCCACCCTCTCTCCGGCCCCCCAAGCGGAGGCGACGGAACCCCTCGGAGTCAGGCTCTGAGCCCTCTTCCTCACTTGATTCTGTTGAAAGTGGGGGTGCTGCCCTTGGAGGACGGGGTTCCCCCTCCTCTCGCCTTCTCCTTGGATCAG
Seq A exon
GTAAGTAGTTGGGAGCTGGAGGGGAGGCCTTAGGGGAGCCCCACCCCTGAGGGTGGAGGTGGTGGGGAGGGCTGCACCTGTCAGAGAGTAAGAACTTCCCGTCCCTGCCCAGGCAGGAAGCGGAGAGAAGGAAGGAGGACTGGACTGAGACTTCCTCAGACAGGTCCCTGCCTGTGAAGAATGAGCAGAAAAAAGGATGAGGCCTCCCTTTTCCCGTGGGACTTAGTGGGAATTTTTCCATCTCCAG
Seq C2 exon
ATCATGGTCTTCGGAAAGCCAAGAAACCAAAAAAGAAAACTAAGAAGAGAAGACACAAGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016589:ENSBTAT00000022067:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGAGTCAGGAGATGAGGAGCT
R:
CGACTTGTGTCTTCTCTTCTTAGT
Band lengths:
236-483
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]