RnoINT0112336 @ rn6
Intron Retention
Gene
ENSRNOG00000005504 | Pkp4
Description
plakophilin 4 [Source:RGD Symbol;Acc:1307840]
Coordinates
chr3:45410187-45411950:+
Coord C1 exon
chr3:45410187-45410315
Coord A exon
chr3:45410316-45411876
Coord C2 exon
chr3:45411877-45411950
Length
1561 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
AATAAAATATTTCCTTACAGGCT
3' ss Score
7.86
Exon sequences
Seq C1 exon
TTGGCAGCACCTCCTCCTCACCAGCACTGTTAGGAATCAGAGAGCCTCGCTCTGAATACGATAGGACCCAGCCACCTATGCAGTATTACAATAGCCAAGGGGACACCACACATAAAGGCCTGTACCCTG
Seq A exon
GTAAGACGCCAGTTGGGTGTGTGATCTGATACCTGAAGGAGTCACCTCTCTGGGTGCTCAGCCAGCGTCCTGGGAACAAGCCTGTGCTTATGTCAACTCGGTCCCAGCAGCAAACCACCTGGTCCCTTCTCTGCTGCTGTTGGATTGTTGCCCTCTCTGCTTGGTTTTAAATAAATCAAGCTAATATAGTTATACAATGACCCCAAATTAAAGAGAGGGCTAGGTCTGGTGATCATGTCTGGCTGCCCCAAGTGCCATTCCCTTTGCTCTTGTCCCCCTCCCACTCTAGCAAGAGATCCTTGTGTATCAGAAGTGAGGGTCCTATGTGGCTCTGCCTGAGCTACATGTGCTCTCCAGACCAGCTCCTCTAAGTCCAAACTGATTGATAACAACCTACTCCATTGACATGTGGGGGAAGGAGCTTGAGTGAATTTAGAATATATCATATGATTACTTTTAAGAACAAAAATAGTTTTGTAGTGTTACTACTTTTATATCCTGTTCAGAAAGATATGCATGAAAAAATATTTTAAAGTTGCCAGCCCAAAAGCTGGTTGGTCCATTCTCCAGATTTAGGAATTAAAACTACTCCAAAGGTTCCAAACAAGTCATGAGCTACTGTAAAGGAAAAGATATTTTTTCCTCAAAAAAGAAAGAAAGAAAGGAAGGAAGAAAAAGGAAAAAGGGGGATGGAGAATACCTATTTATTTAAAAGAAATAAGTGAGAGCTGTGGGCAGCTTAACTGCGGCTGGGGGAGGGTCTGAGTTTTGTTGTTGTCTTTGAATCTGTGATTTCACAGGGCTATTTACTAATTGACTATTGTTACCATGGCAATTAATAGCTCAGAAAATTGCAGATGCTACATTTCAAACAGCAAGCTCTGTGCAGAAGGGAGCACACACAAAGCTGAAATGCAGGCGGCCCCGGGTCTGCAGCAGCCGGCTTCGTTGTACAAACGGCCTCTTGAACACACACCCTTTATCTCTGCTTGTTTCAATAAATCCAATTTGCTTGGAGGATGCTTTATTTTCCTTGTTTTAAAAAAAAAAATTAAAGCCTTCGCTACTTTTAGCAGTAATCCACGAGCGACTAGTGATGTCATCAGGAGTCTGCTCTAGACTCTGGAGGACACTTGCCGCTGAATTACCAAGTTCTTTTTCATTTACAACCTGCTTAGCTATGGCAGACCCAAGACTGTGCCTCTGGGTAGCCCCATTGCCTTAACCATGCCTGAGCCTGCCCTCTCCAGTCAGTCGCCAGGATGTGAATCATGGCTGCCCAGAGGCTCCAGGTTCATTAATGCTGCATTTCCCATCTCTCTGACTCAGACTGTGTGTGGTCCAGGGTCCTGGAAGAGTGACAGTCCCCAGCTCAGCACAAGGAGCTGTGCTACTGCTCAAAGCCGACTGCAGAAATCCCTGAGACTGACCAGAGCTTGACCCAGGGGCCTGGGCTGCTGCCCCTCTGCCTGCGCTGGCACTAGGGAAGACAGGACCCACACAACCTGGTGGACCAGTGTCATAAGCATTAGTTTTAATTTAATAAAATATTTCCTTACAG
Seq C2 exon
GCTCCAGCAAACCTTCACCAATATACATCAGTTCCTATTCCTCACCAGCAAGAGAACAAAACAGACGGCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005504:ENSRNOT00000059246:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.909 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
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGGCAGCACCTCCTCCTC
R:
GCCGTCTGTTTTGTTCTCTTGC
Band lengths:
198-1759
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]