BtaINT0112674 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048098 | PKP3
Description
Bos taurus plakophilin 3 (PKP3), mRNA. [Source:RefSeq mRNA;Acc:NM_001076858]
Coordinates
chr29:51273701-51274264:-
Coord C1 exon
chr29:51274079-51274264
Coord A exon
chr29:51273855-51274078
Coord C2 exon
chr29:51273701-51273854
Length
224 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CGCCCTCCTCCTGCCGGCAGTGG
3' ss Score
8.2
Exon sequences
Seq C1 exon
CTGCCCCTCACGGCCGACGCGCTCACCTTTGCCGAGGTGTCTAAGGACCCCAAGGGCCTCGAGTGGCTGTGGAGCCCCCAGATCGTGGGGCTGTACAACCGGCTGCTGCAGCGCTGTGAGCTCAACCGGCACACGACCGAGGCAGCAGCCGGGGCGCTGCAGAACATCACCGCAGGGGACCGCAGG
Seq A exon
GTAAGGCGGTGGGGCCAGGCCGGACAGGACGGGAAGGCAGGGGCCGCTGAGCGGCAGCAGGAGTGTGAGGTCAGCGCCGCAGACGGCACAGGCCTCGGCTCCTGAGGACGTGGGTTCTGTGCCAGACTTGAGGGAGGCGCCAGGAGGTCTGGGCTGGCAGGGCCTGACCCGCGGGCAGCTCGGGGCGCCAAGCACCTCACTCACCGCCCTCCTCCTGCCGGCAG
Seq C2 exon
TGGGCGGGGGTGCTGAGCCGGCTGGCTCTGGAGCAGGAGCGCATACTGAACCCGCTGCTGGACCGAGTTCGGACCGCTGACCACCACCAGCTGCGCTCACTGACAGGCCTCATCCGAAACCTGTCCCGAAACGCCAGGAACAAGGATGAGATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048098:ENSBTAT00000065717:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTGTCTAAGGACCCCAAGG
R:
ATCCTTGTTCCTGGCGTTTCG
Band lengths:
299-523
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]