BtaINT0112669 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048098 | PKP3
Description
Bos taurus plakophilin 3 (PKP3), mRNA. [Source:RefSeq mRNA;Acc:NM_001076858]
Coordinates
chr29:51275660-51276296:-
Coord C1 exon
chr29:51276173-51276296
Coord A exon
chr29:51275865-51276172
Coord C2 exon
chr29:51275660-51275864
Length
308 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACC
5' ss Score
6.54
3' ss Seq
CCGCATGCCTGTGCCCGCAGGCC
3' ss Score
8.96
Exon sequences
Seq C1 exon
ATTCGATGACATCGACCTGCCCTCAGCAGTCAAGTACCTCATGGCCTCAGATCCCAACCTGCAGGTGCTGGGAGCTGCCTACATTCAGCACAAGTGTTACAGCGATGCAGCCGCCAAGAAGCAG
Seq A exon
GTGACCGTCCCTGCCGACCACGCCCACGGACCCGCCTCACTCAGTGCTCTGGTCCCTAACCGCCCTCGCTGACCCCCAAACTGACTGGGCAGACCTGGGCCTACCCAGAGCATCCCCAGCAGAGGAAGGGTGGGAGGGCTGGACTTACACGTGTCCAAACACACACGCTGACACCGCACACCTGTGCACACACCTGAATATAGACACGCACGCCTGTCACTGTACACACCTGCCTACAGCTGCACACCTCTGCACACACCCATCCGTCGCGTGCACGCTTGTTAACACCCGCATGCCTGTGCCCGCAG
Seq C2 exon
GCCCGCAGCCTGCAGGCTGTGCCCAGGCTGGTGAAGCTCTTCAACCACGCCAACCAGGAAGTGCAGCGCCACGCCACAGGCGCCATGCGCAACCTCGTCTACGACAACGCGGACAACAAGCTGGCCCTGGTGGAGGAGAACGGCATCTTCGAGCTGCTGCGGGCGCTGCGGGAGCAGGACGACGAGCTCCGCAAGAACGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048098:ENSBTAT00000065717:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0051418=Arm=PU(14.6=14.3)
A:
NA
C2:
PF0051418=Arm=PD(80.5=47.8),PF0051418=Arm=PU(80.5=47.8)
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:
GATGACATCGACCTGCCCTCA
R:
CTGTGACGTTCTTGCGGAG
Band lengths:
325-633
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]