GgaINT0047233 @ galGal4
Intron Retention
Gene
ENSGALG00000012561 | PKP4
Description
plakophilin-4 [Source:RefSeq peptide;Acc:NP_001006529]
Coordinates
chr7:35911234-35913571:+
Coord C1 exon
chr7:35911234-35911792
Coord A exon
chr7:35911793-35913379
Coord C2 exon
chr7:35913380-35913571
Length
1587 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGT
5' ss Score
8.02
3' ss Seq
TTACCTCTTCTTGGTTTCAGGCC
3' ss Score
9.95
Exon sequences
Seq C1 exon
CCTTCAGCAAACGTTGCTACCAACCGAGCCATGAGGCGCGTCAGTTCGGTCCCGTCCAGAGCACAGTCTCCCTCTTATGTGGTCAGCACAGGTGTTTCCCCTTCCAGGGGGTCTCTGCGAACATCTCTGGGTAGCGGGTATGGTTCTCCATCAGTTGCTGAGCAAAGATCCCTTGCTTCTCATGCCTATTCATCCACTACTCTGCCAGTACAGCGGGCGGCATCCCCGTATGCTGCACAGAGACCTGCTTCCCCAGTGACTGTGCGGCGGATTGGCTCGATCACATCCAGACAGACAGCAAATCCCAACGGTGGGACTTCCCAGTACCAAGCATCAGCCAGAGTTGGCTCTCCTCTTGCCCTCACTGATGTACAAACCAGAGTTGTTTCTCCACCCCAAACCCAACTGGGATCATCTTCCCCAAAGCGTTCTGGTATGACTGCGGTTCCGCAGCACTTGGGAACAACACTGCAGAGAACAGTTCATGATATTGAACAGTACGGACAGCAATATGATATATATGAAAGAATGGTTCCTCCACGTCCAGATAGCCTTACAG
Seq A exon
GTTAGTAAAAAAAAAAAAAAAAAAAAGTAAAGACACAGTTTAAAGCTTGTTGCAAGCCTGAAACTTGAAATTAAACAAACAAATATTGTAGCAGTAGTACACAACTGTGGTGTATTTTGTAAATGCTGATGTCAAACACTGTGTATCAGTGCAAGAAGTTCAAAGCAAATACCATCTTTCTCTCCGATTTAGCAATCAAGCTAGCAATGCATTGCATTAAGTTGCATGTTCTGAGGTTTACGTGGCAGTTCCTATTGAGATGCAGTTACTATGTGCTTTAAGTTATTTGCGGTTGCTGTTTTTGTCTGACCTTCATCTAAAGGAGCACAAACAGGTGTGATCTTGCAGTTAGGACTGTATGCTCTTCTGAGCAGTGACTGCAACATTTATTTTCTTTTAAACTATTATACTTCAGGCAATACCAAAATAATCTTATTTCGCAGCAAACAGAATAAGGGGTCTTCTCTCTGACCTCCATTTGCAAGGCTTAATAATCTACCAATTTGCTATGGAAAAAAACTGGATTGGTCACGAAAGGCAATTCAGTAGCAAAAGTGAACGCAGTCCAGTGGATCACATAGTTTGACATAGCAGTAAATCTGTACTCTTAAAGTACTGTTAAGGTACTTTACAAATATCAGTGCTTGAGAATATTTTCTTCTCTAAACAGGTGAACTAATATATCCCCTTAAAAGAGATGAAAAGACTTACTGGGGTAAATCAGTGATTCAGAAACAGATTTTAAGTTCAGTGCATTTGTAGTTTTAGCGAAATAATTAGCAACTGCTGTAGTCATGCTTAGCAACTCATTTTGTAGCCATTTTTACTATAAACTTTCCAGGAAACAGTTATTACTTTCCTGTGCTCAATCCTCCAGCGAGAAAAGCCTTACCTTTCCTCATATAAAGTAGTCCTCATGTTTCTTTAGGGGAATAATTTAATACTGAAATCTTTATTGGGTCCAGGAGAAAGGTTAGTACTGATGCAGCTGTGCTGTTAGTACTGTCCAGAGCTGCTCCCTGCTACAGAAGCTGGATGAGAGGTTGGATCTGGCAGTGCCGCAGCGATAGCAGTAAGCCCACTGCTGAGGAAATTACGTTAAGTACAGCAGAGGTAAAATAAACAGAACTCAAGGTAGCCAGCTAAAAGGAAGGTGAAAAACAAGCATCTCCTACAGTTCCAGCAGAACAGGATATAGAAACACAGAATCATCTAGGTTGAGAAAGACCCTCAAGATCACCAAGTTTAACCACCAGCCTGACCTGCTGTGCCCAGTCAGATTCACCATGCTCAGTATGAACTGTGTGTGCTGACCTGGCTTCCACTCAGACTTTAACTGTAAATGCTGCAGTAAAAAATTGAGTTGGAAAACTTAAAGTTGGCAGTGTTTTATTGAGGGAATGCTGATTTGTCAATGAATGTTTTGGTATGCATCATTTAACAATGGAAAGAAGTTTAAGGCAGAAATGTTTCTTGTGTAGCTATAATACATTTTTTTTCTTGGCTAAAGGAAGGAAGATACAAGCATCGCTGCTTTACTTTTAATCAGTGTGGGCTATGTACATATTTACCTCTTCTTGGTTTCAG
Seq C2 exon
GCCTGAGGAGTTCGTATGCTAGTCAACACAGTCAACTAGGACAGGAATTACGATCAGCTGTATCTCCTGACTTGCACATCACCCCTATCTATGAAGGCAGAACTTACTACAGTCCTGTGTACCGTAGCCCAAATCATGGAACGATTGAGCTCCACCAGGGGTCCCAGTCAGCACTATATCGAACAGGGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012561:ENSGALT00000020513:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.955 A=NA C2=0.726
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGACAGCAAATCCCAACGGTG
R:
GGGTGATGTGCAAGTCAGGAG
Band lengths:
351-1938
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]