BtaINT0112661 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002651 | PKP2
Description
plakophilin 2 [Source:HGNC Symbol;Acc:HGNC:9024]
Coordinates
chr5:77436896-77438100:+
Coord C1 exon
chr5:77436896-77437060
Coord A exon
chr5:77437061-77437926
Coord C2 exon
chr5:77437927-77438100
Length
866 bp
Sequences
Splice sites
5' ss Seq
GAGGTATAT
5' ss Score
7.3
3' ss Seq
CCATTGTGTGTGTGGTTTAGCAA
3' ss Score
6.49
Exon sequences
Seq C1 exon
GCCTTTTTTAACTGTGTGAGCATTCATCATAACCTCTCCTACCAGCTGGAGGCACAGCTCCCAGACAAATATTCCCAGAGTATTTATATTCAAAACCGGAATATCCAGGCTGACAACAACAAAAGTATTGGGTGCTTTGGCAGTCGAAGCAGAAAAGTAAAAGAG
Seq A exon
GTATATTGGGAAGTCTTTGAAAGAATAAGTGTGCGTGTGTGTTTCTAAGTACTTAGTGTATGTCAGGCTCTATTTTAAGTTCCTTTAGTCTTTGTATCAGTCCTATGAGGTGTGTATTAATATCTTCCTTTACTGATGAGGAAACAGAGATACAAAAAAGTTAATTGATTTTTCCAAAATAATCAGCAAATTAGTGGAGGAGATAGAATTCCATCCCAGGCAATCTGGCCCCAGATTTACATTGTTAGCCATCAAACCATACTGCTCTGTGCCCCGCAGTTTAGGAAGTAAACTTAATACCGTGTGGCCAGTGGTATAGCATTATCTTAACATTAAAAGAAGCCCAGACATTCAGCTTTAAATGTTCTAGAAAACAAACAAGACATCCTAAAAGCAAACCGCATAGGAAGGACACCTTCCAGACTGGCATTTTATGAAAATTGAAGGAATGTGATCTCTCTTACTCCTCAGAGTACCACAGTGTTGATGAACTTAGAGAATACTTGGTAAATTTAGAATACTGATGCTGTCCTGGACAACTTCACAAGACTCTGTGAGAAGACGCCTGTTTTTCTTATCTTCGGAGCAGTTGTGACTAATTTAGCTTTTAGCTTAACAGCAGCCTGAAAAATATTCTAGAACAGTCTTTGCTTAATTCTCTGTATTCTCTCTCATGGTGAAGGAAAAATAATCATCATGGGCTAAAAGTTAAGTGATTGTAAATCATACATGTGTGCCTTTTTAATGTTTAAGGTCTTATTAGTCTCTCTAGACAAGACAATACTTGTGGTCTCTTGGTTTGGGTATGGAATTGTAGAAATCACTTGAAGTCTTTACTTTTGGGTTCCATTGTGTGTGTGGTTTAG
Seq C2 exon
CAATACCAGGACATGCCAATGCCAGAGGAAAAGAGCAACCCCAAGGGCGTGGAGTGGCTGTGGCACTCCATTGTGATACGAATGTATTTGTCCTTGATCGCCAAGAGTGTCCGAAACTATACTCAAGAAGCATCTTTGGGAGCTCTCCAGAATCTCACAGCAGGAAGTGGACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002651:ENSBTAT00000003435:8
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=0.224
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0051418=Arm=WD(100=72.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTAACTGTGTGAGCATTCATCA
R:
TGGTCCACTTCCTGCTGTGAG
Band lengths:
334-1200
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]