BtaINT0112670 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048098 | PKP3
Description
Bos taurus plakophilin 3 (PKP3), mRNA. [Source:RefSeq mRNA;Acc:NM_001076858]
Coordinates
chr29:51275143-51275864:-
Coord C1 exon
chr29:51275660-51275864
Coord A exon
chr29:51275318-51275659
Coord C2 exon
chr29:51275143-51275317
Length
342 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGCC
5' ss Score
3.48
3' ss Seq
CTGTGGCCCACCCACCACAGGGA
3' ss Score
6.39
Exon sequences
Seq C1 exon
GCCCGCAGCCTGCAGGCTGTGCCCAGGCTGGTGAAGCTCTTCAACCACGCCAACCAGGAAGTGCAGCGCCACGCCACAGGCGCCATGCGCAACCTCGTCTACGACAACGCGGACAACAAGCTGGCCCTGGTGGAGGAGAACGGCATCTTCGAGCTGCTGCGGGCGCTGCGGGAGCAGGACGACGAGCTCCGCAAGAACGTCACAG
Seq A exon
GTGGCCTGGTCCCCGCCCGCTACCCGCCCCCCACCCCCTCCCGCACCTCCCGCCGCCTCTTCCCTCGGACCCCACGGCCATGCCTTGGCACATCTCTTTAGAGCCAGCCTCCACCCCAGGGCTCGTGTCCCCAAGGGTCGTCCTCTCTGCCCTACCGCAGCCCCGTGACCCTCTGGGTCACACCCAGGCTGTCCCCAGGAAGGCTGGTGGGTGAGGCTGGCAGTGCCCCGCAGGGACAGGTCAGGAGCCTCCTCCCTACCACCTGAGGAAGACAGAGGGGCTGGAGGCCTCGGAGGTCCCCAGAGGTGGTGCCTGACCACGACTGTGGCCCACCCACCACAG
Seq C2 exon
GGATCCTGTGGAACCTGTCCTCCAGCGACCACCTGAAGGACCGCCTGGCCCGGGACACGCTGGAGCAGCTCACAGATCTGGTGCTGAGCCCCCTGTCGGGGGCGGGCGGGCCACCCCTCATCCAGCAGAACGCCTCTGAAGCCGAGATATTCTACAACGCCACCGGCTTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048098:ENSBTAT00000065717:5
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=0.034
Domain overlap (PFAM):
C1:
PF0051418=Arm=PD(80.5=47.8),PF0051418=Arm=PU(80.5=47.8)
A:
NA
C2:
PF0051418=Arm=PD(17.1=11.9)
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:
GTGCCCAGGCTGGTGAAG
R:
GCCGGTGGCGTTGTAGAATAT
Band lengths:
354-696
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]