BtaINT0112666 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048098 | PKP3
Description
Bos taurus plakophilin 3 (PKP3), mRNA. [Source:RefSeq mRNA;Acc:NM_001076858]
Coordinates
chr29:51272554-51273193:-
Coord C1 exon
chr29:51273106-51273193
Coord A exon
chr29:51272931-51273105
Coord C2 exon
chr29:51272554-51272930
Length
175 bp
Sequences
Splice sites
5' ss Seq
GCGGTATGT
5' ss Score
9.45
3' ss Seq
GGGTCCCCTCTCCACTGCAGAAG
3' ss Score
6.81
Exon sequences
Seq C1 exon
CCCTGACAGTGAGAAGTCCTCCCGGGCGGCCTCTAGCCTCTTGGCCAACCTGTGGCAGTACAACAAGCTCCACCGAGACTTCCGGGCG
Seq A exon
GTATGTTCCCGTGGCCCAGGGCAGGCGGGGCTGCAAGTGTGGGGCACGGAGGCGGGACAGGAGGGAGGGACAGGGAAGCCACGCTGCACAGGAGGCCTGGACGGCCAGGGCCTGCTGCCAGCACACTGGACGCGGGGCAGCACAGCCCTGACTGTGGGTCCCCTCTCCACTGCAG
Seq C2 exon
AAGGGCTACCGGAAGGAGGACTTCCTGGGGCCGTAGGCGAAGCCTTCCTGAAGAAGGAGAGTGCGATGTGACCCAGCCTCCTAGGGAAGGGCTCAGCTCAGGGCTGCTCGCCAGCCGGCCTGGAGGAGAAGGTTGAGGATGGCCCAGGGGCCTCTCGCTGGAGCCCTGTCCACATGCAATGTGAAGGCCTGGGCCACGGGGGAGGGGAACGAGGGCTTGCAGCTGGGGAATTGGCTTCTGCGGGGCATGGGGGGGCAGGGCTTGAGGCTGCTCTGATGCGTGGGGTGGTGGCCAGGTCACACTGGAAGAGGTGGTGCTGGCTGTGGCCCAGCGGTGCCTTGGGACAGCCAGCAGTGGGAATAAAGGTGGCCGTGAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048098:ENSBTAT00000065717:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.167 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:
ACAAGCTCCACCGAGACTTCC
R:
AATTCCCCAGCTGCAAGCC
Band lengths:
258-433
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]