BtaINT0118372 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016589 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:25031]
Coordinates
chr5:30384066-30384588:-
Coord C1 exon
chr5:30384478-30384588
Coord A exon
chr5:30384187-30384477
Coord C2 exon
chr5:30384066-30384186
Length
291 bp
Sequences
Splice sites
5' ss Seq
GAGGTCCTG
5' ss Score
-2.13
3' ss Seq
CCTGGCCCATCCTCTTACAGCTC
3' ss Score
11.78
Exon sequences
Seq C1 exon
AGGGCCCTGTGGAGCGAGCATGTAGCCCCTGACGGGCGCATCTACTACTACAACGCTGACGACAAGCAGTCCGTGTGGGAGAAGCCCAGCGTGCTCAAGTCCAAGGCAGAG
Seq A exon
GTCCTGAATGGGGCTTTCTGGCTCTTTTTTTCAGCTGCCCTGACCCTTCCAAGTCCTTGGCCTCCCTTGAGTCTCTAACCATACTCATGGTTCCTCTAATCCTAAGATCCCTGACCGTTCCCCAACCTTCCTAGGATCTCAAGAAGTCCACCTTCCCTCATCTTGAGCCAGGCCAGGTGGTACCTAAACACTTCTGTATACCCCCTCACTGGGTCCCCTCACTTAGCTCCCCCAACTGTGGCTGGCGGGTATGCCCAACCCACTGATGTTTCCTGGCCCATCCTCTTACAG
Seq C2 exon
CTCCTGCTGTCCCAGTGTCCCTGGAAAGAGTACAAGTCGGACACAGGCAAACCTTACTACTACAACAATCAGAGTAAGGAGTCCCGCTGGACCCGGCCCAAGGACCTGGATGACCTGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016589:ENSBTAT00000022067:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.378 A=NA C2=0.683
Domain overlap (PFAM):
C1:
PF0039721=WW=PD(90.3=75.7)
A:
NA
C2:
PF0039721=WW=WD(100=73.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTGTGGAGCGAGCATGTAG
R:
CCTCCAGGTCATCCAGGTCC
Band lengths:
228-519
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]