BtaINT0112671 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048098 | PKP3
Description
Bos taurus plakophilin 3 (PKP3), mRNA. [Source:RefSeq mRNA;Acc:NM_001076858]
Coordinates
chr29:51274584-51275317:-
Coord C1 exon
chr29:51275143-51275317
Coord A exon
chr29:51274702-51275142
Coord C2 exon
chr29:51274584-51274701
Length
441 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGC
5' ss Score
9.1
3' ss Seq
TCACCTGTCTCCACCCGCAGGAA
3' ss Score
12.54
Exon sequences
Seq C1 exon
GGATCCTGTGGAACCTGTCCTCCAGCGACCACCTGAAGGACCGCCTGGCCCGGGACACGCTGGAGCAGCTCACAGATCTGGTGCTGAGCCCCCTGTCGGGGGCGGGCGGGCCACCCCTCATCCAGCAGAACGCCTCTGAAGCCGAGATATTCTACAACGCCACCGGCTTCCTCAG
Seq A exon
GTGCGCCGGGCGGCCGTGGGGCCCTGAGGTCCGAGGGACAAGGCGGAGCCACTGGGTTGCGGGGGGCGGGGGCTCTGGGGGAAGTGGACGAATCCAGCAAGGCAGAGGTGCTGACCCACGAGTGGAGTGGGTCACCAGGTGTCCTCCCCCCAGCCAGATGTCAACAGACTGCAGGCTCAGGTTTCTTTAAATCAGGGACTTGATCTGACATTTCTAACCTGCCCCGACCCCAGATGGTTTGAGGAGTGGATGGGGGCAGGCGTGCAAAAGCGTGGGAGCGACAGTGTCCAACAGGGGCCAGGAGCAGGAGCTGCTGGGGGCAGGCCCAGCGCGCGGTGGGGAGGGAATCGGGGCCCAGGAGCTCAGCCTCGGGTTCAGCTCGCTGTGGGGTGGCTCTGCCTGGGGTCCCTGTGCCGGCCTCTCACCTGTCTCCACCCGCAG
Seq C2 exon
GAACCTCAGCTCCGCCTCCCAGGCCACTCGCCAGAAAATGCGTGAGTGTCACGGGCTGGTGGACGCCCTGGTCACCTACATCAACCACGCCCTGGACGTGGGCAAGTGTGAGGATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048098:ENSBTAT00000065717:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0051418=Arm=PD(17.1=11.9)
A:
NA
C2:
NO
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:
GGATCCTGTGGAACCTGTC
R:
TATCCTCACACTTGCCCACGT
Band lengths:
291-732
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]