BtaINT0112687 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013773 | PKP4
Description
Bos taurus plakophilin 4 (PKP4), mRNA. [Source:RefSeq mRNA;Acc:NM_001191491]
Coordinates
chr2:37826356-37829762:-
Coord C1 exon
chr2:37829612-37829762
Coord A exon
chr2:37826552-37829611
Coord C2 exon
chr2:37826356-37826551
Length
3060 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGT
5' ss Score
7.76
3' ss Seq
AGCTCTTTTGTCCTGGGCAGGGA
3' ss Score
8.06
Exon sequences
Seq C1 exon
TTCGCAGCATATATCCGAGCAGCCGTCCGCAAAGAAAAAGGGCTCCCCATCCTAGTAGAGCTTCTGAGAATGGATAACGATAGAGTTGTTTCTTCTGTGGCGACTGCCTTGAGGAATATGGCCCTAGATGTTCGCAACAAGGAGCTCATAG
Seq A exon
GTATGTTCTGGTGACTTGATGAACTCTAAAGAGAAATGACAGCATTTATAAAGCTCTTCTTTTGATTTATAAAAATATGACATTTAAAATGATTAGCAACTGAGTCCTAGTCCCTGGTTTCTTGGTGTATTTGGTACCTTTGTGTCTGTCCTTCCTGACCACTCCATTTCAGCGAGAGGTAGGCTTATTAATTAAACATTGATCTGGAAGGTACGTGTTCAGAAAAGCTAGCAGTTTCAGTCATACATTACAGAGCTACTTGGTAGATTTGGCGTGACTGTTTCCCAAGAGAGATTCATTTCTTAAACCACAAAAAAAAAAGGTTTGATTCTCACTTTTCTGATTTTTGAGACTTATATCTGCTAATTCACCAATACTACCATGTTCTAAATTTTACAAAGAAATCACATGAATGTTTTATAGCTTTTCCTTCTCAGATTTGTGTAAGTGCTCACACCAAAACAGAGCCAGTGCCCCAAGGCCTGACCCCAGGGCAGGGTCAGGATGAGGGAAAGGCAAATGAGGCATATAAGGTACAAAATTATAGGAGGCATTCACCCTTAAATGTAGCTAGCACTTGCATGAACTTGAGAATGAGCTCCTCTTCAAAGTTCTGCACTCTTGGCAGCTTACCTTGTTTGCCTCCTTGGGATGGCCACCATCCCAAGTAGAGTGTGGCATACAGAAAAGATCAGCGGGCCTCAGGTTAAACCCTGGATCCACTGCTCACTGGCTATGTAACCTGGGGTGTCCTGTATTGAGCCCACCAGGCTCCATTCCTTCATCTCAATTGAAAACCCTTCCTTGGTTTCCATCTCTGAAAGGAAGCTGCCCATGCCAGCTCTCCTCACAATGGATTTGCTGTGAAAATGCAAGTTCCACGCCAGACCCATAGCTGGTGACGGGTCAGGGGAGGAGGAGGAGAAATTAGACAAGACCTTATGTGGATTAGTGAATGTATGTTGAACTCATTAAAATGCCCATGAGAGATAGGGAGAGAGGAAAGGAATAGGGGCCAGAAGGTTTACCTTACAGAGTGACAGAATTCTCTATGGCCCCTCACACAGTGCCTGACAGCAATGCTGTTTTAAGTCATTGCCTGGATTATCCTGTTCTTAAAACACCATTCCTCCATGGAGCCAAACTGTACCTCACAGAGAGGAAAGGAGCTTCTTCCACAGCCTGTTCATACTCCAACTCATGCCTGATTCCAGTAGATGTGTTTATAGCTCTTGAAGTTTCCACATTTCCTTGAGAGAAATCCTCTAGGTCCCTAAAGAGAGATTTTTAAAGTTATTTCTGTTACATTTATATTATTTGAATGTATAGTTTGGGAGTTCTTACTGCTAAAAATTAAAGGGTTGGCCACAGATGCCTTGCAGCCTATCATTCCACACATGGAGGAGAGAGTGGGAGAGCAGAGGGTGCTGGCCAATTCCATAAGAGCCAAGACCTGTGGGGAGAAGCAGTGTGCATTCCGGGGCCTCGCCTTCTCTCAGTGCCTCCCTGTGTTTTTGAGAGTTCCTCACCCGCTTTTAAACTTCAGTGAGCATATTCTCCCTCCACTGATGAGCTTTATTTTACCCGCGTTATTTACTCAGGAGTCACTTTTTCTTGTTTCCCCATGAAGATCCCTTCCTTCCTAGGCAGTCTGAGCGCCTCCCGGATCTGACTCTGATTTACCCAGCATTTCTGTTCCTAAGAACCACTCCCTTCACTCTCCTCACGTCCAGCACTAGCAGTGGACTCTGTCTCCAGAGATGTTTCTTCACAAGGAAACACAGTTTTGTGAGTTCACAAAAGTTCCTGCATATTCACCTGAGTCTGACCAAGCTAGCTGTCTGGGCCGCAAGCTCTGAGAGAACTGCTAGGGTCGCTCACAGATGGAGTGAGCGGCCTTCTCCCAGACGTCCAGAGTGCAGTTTAAAACTATGCCTTAGCAAAATGACAGATTACATGTTGCGGACCTGCTGGTCGTTCACAAGTATTCACAATCACAAGTGCTAACTTATCATCTTTTCCTAAAACCCATATTTATCTTCTGGCTTAAGATGTCATCACTGTTTTTCCACTCTTGGTAACAGTATTCTCTATGAGTAAAGCTCAAGTCTTCCCTTGACATGCTGTAAATCATGGAGCTTGTATTCAGGCACTATCTTCTCCTGCTTACCACTGTATATAAATAGGTCTTCAATAAAAACCCCATTTAGCATCCACTCAATTATTAGCATGGGGGAAAAAACTAAGAAAATATTTACTTGTGCTTTAGTTAATTTCCAGTTTGTCAGTCAGTAAGTGAGATGGCAAAAGCTCGAGATAATTGCATTTTGGAAAAGAGTAAGGGAAATTGAGGGCCTGTAGGGAAATGCTTCAGGAGCGAGGGGGCTCCCCTGCCTTGTCCTGTTGGGAACTTTATTATTACATCACTCCTGAGACATACAGCATACTCATTCATACCAGAATTGTATTTGTGTCTTCTTTAAAAGAAACAAACACGTTGTTACTGATGTCAGATGCCAGACCGATAGAAACCCTCAACTTGATGAAAATATGTAACTACCCATTTCACATGTTGAGATCTAGAAAGATGTCATGAAAAGTATTTTTGGCAGCCTTATTTGACCAACTTAAAACCTATTCAAAAAAAAGTTTTTAAAAGCTTTAAGAGGAAGTTGTAATTGTGATACATAGGAATTGAATGGAGAACAATATTTACTATCATAATTCCTTTATTCTCACTGTTCATGAAAGTAGTGGAAACTAAAGCAGTGTGATTAGTACACCAGTTTTATACCCTGATTTACATTTTCTTTTAGCAATTTTCAGTAAAGTTTTATAAATCAAATCATTTCCCCAAGTGGCCTGGCTGTGATGTTAACCTGCCCCTTACAGTTAAAATGTTTGTCATTTCCTTTTTCACTGTGGATTTTTTTCTTTCCTGTTATTGTCTCTTTTGAGGTTTTATCTTAAAGAGACCATGCAATCACAATTTTTCAATAACAATAATAACAAAAACCAGGTCCCTTCCAGAATCGGAATGAGCTCTTTTGTCCTGGGCAG
Seq C2 exon
GGAAATACGCCATGCGAGACCTGGTCAACCGGCTCCCAGGTGGCGCCAGCCCCAGCGTGCTGTCGGATGAGACCGTGGCGGCCATCTGCTGCGCCCTGCACGAGGTCACCAGCAAGAATATGGAGAACGCCAAGGCTCTGGCTGATTCGGGAGGCATAGAGAAGCTGGTGAACATCACCAAGGGCAGAGGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013773:ENSBTAT00000018330:20
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=0.015
Domain overlap (PFAM):
C1:
PF0051418=Arm=WD(100=74.5)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]