GgaINT0114675 @ galGal4
Intron Retention
Gene
ENSGALG00000012913 | PKP2
Description
plakophilin 2 [Source:HGNC Symbol;Acc:HGNC:9024]
Coordinates
chr1:59005456-59007288:+
Coord C1 exon
chr1:59005456-59005617
Coord A exon
chr1:59005618-59007114
Coord C2 exon
chr1:59007115-59007288
Length
1497 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAG
5' ss Score
8.27
3' ss Seq
TGATCTGTTTACATGTTTAGAAG
3' ss Score
5.38
Exon sequences
Seq C1 exon
GCCACAGAAAATTGTGTGTGCATTTTGCACAATCTTTCCTACCAACTAGAGGTAGAACTTCCTGAAAGCTATGCCCAGAGCATCTATATACAAAGAAGAAATATTTCTACCAATGATCGAACACCAGGCTGTTTTGGAACACGGAGCAGAAAAGTGAAAGAG
Seq A exon
GTAAAGCACATGTTTGGTTACATCTCATTTTGTTAATCAGTTGTAGCAACTTCTGGAGAATATAAGGCTGTGATCTAATTAGGTTGCTTCTCTGTTGGTGATGCGTATGGTAGTGAGACACACCCTCAAAATGAGAATTTATCGATAGCTTTTTCTAACATTCATTATCCTATTAGATGTCTGATGGAACAAATGACAAAGCAATTCACAATTTCATTAGTTGAGAAATACTGCCTCTCAGCTTCATTACCTGATGGATCTAACTGGAGTCTGCACCATGTTCAGCAATTGTGCAAGTGTCCTACCGATGACTGGCTATTGTAGCAGTTTCACAGATGGAATTAGCACAAGTTGATTTGCCTTCTTCGTGGCTTTTGGACTTCTCACAGATCCAAATATTCTGGCAGCTGGAATTGTTGGGGAGAAAAACAGGTACCAGGGAGGGGGAAAGGGAGATAGGAGGATTTATGCTCCTCCCCCGTCCATTATTTTTGCTGGAGTCTATTGCTTCTTCTCCTGTTCCATACAGAGTACAGCTTTAGCATGCTATTTCTCTTTCTCCTTCAGCTCAGCCCCCAATGTCAATAGCTAGAGATGCAAAGCATCTTCCCCTTCACCTATCTCCCATTTTCAGATGGAATGGTCAGTACAGTTAAATACTGGAATTTTACAGGTTGCCATTAGTGTTCACAACTTTCTACTTGCCAAGGAGCTTAAAATCTAAAGGAGTGTGAACATGGATCTTCTGGTCATCAGTAGCATAATTTCAATTAATAAAAGTGAAACAAAATCAGACCTGCTCCTAGACTATGAATGTTAGGGAAAATTAGGGAAAATATAATTATTGCAAATTAAACATACTTTAATCAGTCATCAAACATATCCATACTCCTATGACAAGAAGACTAGCAGTGAGTGCTCTTGGCTATGTGTTATCAAATAGCAGATCGTTTCTCCTGGAGAATACGTCCCTATTTCTCCACAGCGGATTACTTCAGGCTCATTCCCTGAATCATCAAAGATAAGAAATGTTCTCACACATGAGCCTATTGGTAAAAATTATTGTTCCATCTTGACTTTCCAATTGCCATGTTTGAACTCATGTGATTGATAATAGATCTTGGGTATGAGTACTTTTTAACCAATATCCTAACATACAGTAGTAAAAATGAAAGCATTCTTCACTTTGAATTGCAGTCCCTGATCCAGCTAACAAAAATGGTATAAAAAACAAGGAAATAAACATGTATCTTAGAAAAAGAACTTGAATCAGCTTTTAATTCATTTTTAGACTCTTTGATTATTAAAATATCAGTGATAATACAACACTAAGTGTCTATCTTAAAATAATGTTCATTTTCATTCTCATGAAGATTCTCTGTAATGAGCTCCACAAAATCATCTGGTCATAGAGTTACAAAATTGCTAGTTTAGATTGTGATGCATTATGTCATATAAGGTTACTGGTTCTAACAGCTGATCTGTTTACATGTTTAG
Seq C2 exon
AAGCAGCAGGACATCCCGCTACCTGAGGAAAAGAGCAATCCCAGAGGTGTGGAGTCACTCTGGCATTCCACACTGATTAGGATATATCTCTCCTTGATAGCAAAGAGTACCAGAAACTATACCCAGGAAGCATCCCTGGGAGCTCTTCAGAACCTCACAGCTGGTACCGGACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012913:ENSGALT00000021059:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.241
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF048268=Arm_2=PU(38.6=67.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGAAAATTGTGTGTGCATTTTGC
R:
GGTACCAGCTGTGAGGTTCTG
Band lengths:
327-1824
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]