BtaINT0112691 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013773 | PKP4
Description
Bos taurus plakophilin 4 (PKP4), mRNA. [Source:RefSeq mRNA;Acc:NM_001191491]
Coordinates
chr2:37817715-37819549:-
Coord C1 exon
chr2:37819421-37819549
Coord A exon
chr2:37817789-37819420
Coord C2 exon
chr2:37817715-37817788
Length
1632 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
CATAAAATATTTTCTTACAGGCT
3' ss Score
7.97
Exon sequences
Seq C1 exon
TCGGCAGCACCTCGTCCTCACCAGCACTGTTAGGAGTCAGAGACCCTCGCTCTGAATACGATAGGACCCAGCCACCTATGCAGTATTACAGTAGCCAAGGGGATGCCACACACAGAGGCCTGTACCCTG
Seq A exon
GTAAGATGCCAGTCGGGTGTGTGATAGAGTATCTCGAAAAGCCGCGTGTCCCCAGGCGCTTGAACGGCAGCCTGGGAGGTAACCTCTGCCTGCCTTGAGATGGTCCCCCAGCAGCAAACCATGCTCCACTGTCTCCATCTCCTTCCTGCTTCGGGGGCTGTTGCCTTTCCCACTTGTTTTAAGTAAAACAAGCAGAGGCAGTGGTCTGCTGACCGCAAATAAAAAGAGCACTGTATCCGAGTGAGAACGCATTTCCCGCTCCCGTGCAGCGCAGGCCCTGTGTCCTGCCCCCTCCCCACTCCCCTGTGTGTTCCAGAAACCTGTGCTCTGTGACAGTCGGCAGGGCCGATCTCCTGGACCGACTCATACATTCAAACCTGCGGATGGGGGTCAATTCCATTTGCATTTTCGTGGAAAAGTTTGAATGAATAACAAAATATATAATGTGATTCTCCTCAGAGTGATTATTTATTTTTTAAGAATAACAAAAGTGATGTTGCACAGTATTATTTTTATGTCCTATTCAGAAAGCCGTGCATATAATTTATTTAAAGAATGCCAACCTGAAGGGTTACCATGACTTCATATTATCTCCATTCTCAGCTATCTTGCAAATTGAAACTCCTCTGGAGGTTTCAAAAAGGAGGGGGACGCTCCTTTCTCAAAAAAAACTATTTATTAAAAAGAAATAAAAGCTGGTGGCAATTTAACAACTGCTGGGGGAGCAGTCTCAGTTGTGCTGTTGTCTTTAAAATTGTGATTCCACAGGACTATTTACTAATCGACTGTTGTTACTATGGCAATTAATAGCTCAGAAAATTGCAGATGCTACATTTCAAACACCACGCTCTTTGCAGAGGAAATGCACATACCAACTGAAGTGCATTGTTGCTTCAGGTTTGCAGCAGCCTGCTTTATTTTAAAGATCGCCTCCTTAGCATGCGCGCCCTTCTGTATCTTCTTTGCTTGCTTCAATAAACTAATTTGCCTCAAATATGTTTCATTTTCCTCATTAAAATAAAAATCTTTGCTAGCCTTAACAATACTAGAAGGGTAACCAGTGACATCATCAGAGTCTGCTGTGGCCTCTTGAAGACAGCTATCTGGTTACCAGGTTCTTTTTAAGACATACTCAAATATGGCAGACACAAGACTGTGCCTTCAGGTGGCCGGCCTTTTAGAACACAGGCTGTGCCTGCTCCTTGCAGGACCTGGGATTTTGAATCAAGGCTGTTCTGAGAGCATGGAGCTTGTTCCGCTTTGTTTCCCCTCCCCCATCTGAGGGTGGGGGCAAAGCTCAAGAGCCCTGGAAAAGCCATGTTCCCCGGGCTCCGGGAGCATGTCTGCTGTTCAGAAAGCCAGCCAGCGAACATCTACACAGGTGGGAAGAGCTCCCCATAGTGACCAGAGTTTGAGAAGGAATCCTTTTTGGATCTGTGCATTGGCATTGCTCTTTGGTGAGACACGCAGGCTTGATCCGGGGCACCCAGGCTGCTAACCGTCTGGGGCTATGCCATGCCGGGAAGGCAGGGCCTGTCGGGCACACCACCAGCCCTAGCCCTGGGAGTCCATATGACCTAATGGACCGGATAATGAGCACTAGTTTTAATTTCATAAAATATTTTCTTACAG
Seq C2 exon
GCTCCAGCAAACCTTCACCAATTTACATCAGTTCCTATTCCTCACCAGCAAGAGAACAAAATAGACGGCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013773:ENSBTAT00000018330:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.932 A=NA C2=0.760
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCACCTCGTCCTCACCAG
R:
CTGTAGCCGTCTATTTTGTTCTCT
Band lengths:
198-1830
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]