GgaINT0047234 @ galGal4
Intron Retention
Gene
ENSGALG00000012561 | PKP4
Description
plakophilin-4 [Source:RefSeq peptide;Acc:NP_001006529]
Coordinates
chr7:35913380-35915342:+
Coord C1 exon
chr7:35913380-35913571
Coord A exon
chr7:35913572-35915125
Coord C2 exon
chr7:35915126-35915342
Length
1554 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TAATACTAATTTTATACTAGGAG
3' ss Score
4.41
Exon sequences
Seq C1 exon
GCCTGAGGAGTTCGTATGCTAGTCAACACAGTCAACTAGGACAGGAATTACGATCAGCTGTATCTCCTGACTTGCACATCACCCCTATCTATGAAGGCAGAACTTACTACAGTCCTGTGTACCGTAGCCCAAATCATGGAACGATTGAGCTCCACCAGGGGTCCCAGTCAGCACTATATCGAACAGGGTCAG
Seq A exon
GTAGGTAAAGGGCTTACAGAGCTCTTCCATCAGCTGTACCAGAGCTGCGCTTGATTTATGTAGTGGAGCTTTTCTGGGGCCTATGGCATATAGGAGATAGGTATCTTTGATTTCAAAGTAGAAACTATATGCTGTAAATCAGTGCGGGTAGAAACTAGGGTTGGAGGTACTTAAATGGCCAGCAGGAATTTAAAGTTTTTATGATGTTTGCAGGAAATGCTTTGGCTGTATGTCAGTGTCAGGTTAGGGTCACAATATGTTCTCTGATGGCATGCACTCAGGTACATCCAAGCAGAGTATTTCATGACATAAACATTTTATTGCTTCCTCCTTCATTCTCTGTGCATCATTCAAATACAAGCTGAGCGTGTTCATTTTTTCCTTTTTAAATTCATCAGGGCAGTAAAATGATAACTTGCACAACTAAATTACCTACCGTATCTTTCACAGTAAAAATTCAGTTTCTACCCAACTTCCTAGCTGAGGATAATGTCAAAATGCTGCATCTGAAGATAGTGTAGTGAAAATGAAATATTTCTGTAGTAATTGGCAGAATTGCTACGGACAGATTATGAAGTGCATAGGCATTATAAGTAGTTTTAGAACTGATTCTCTGTAAAGAGAATGGTTGATTAATTTATGTAGTGGAGTAATTTCTAAAAAGTGTGGAAGTAATAGAGTTATCTAACTAATAGAAATATTAGAAATAGAATAATTAGAAAAATAGAGATAGAAATATTTACAGAGAAGCGTCCAATTCATATGTCTTATATTTGTACATCTGAAAACTGCTTCTTGGTGCATTTCATTCCTGAAGTACAAAGAGCACAGGACAGTGAAGGAGGCAACGGCCTTTGCAGTTATCCTCTCTTCCACAGCACGCAATAGATACAGTTTGTCAAGATATGCCAGTATATCTACCAGACATAGCTAGAAATTTGAATTCTCTGTTTATTTGTCTACCTGATATCAGTTACTTTGGAAGAAAAGAAGCTAGCACAACAGTTCTGCTAACTCAGGAAGCTACATATGTGTTCCTGACTTTGCAACTATTAGCTTAATACTTTGAAATCATCCCCTGGCATGGGGGGAATAAAAGCTAGCAAGCTTTTATTCAGGGAAATGTACAAGTAATTGTGAAAAGTAAAATAGAATACAAACTATATACATTTTTGTTTAATTCTGTTTCCTTTTTCTTTTTAGTACTGTTGGCAAATTGAAGTTACTGTTGGTAATTGAATTTTATTATACACCTTAAAACATTTTGCATCCTAATTTCTCCTTAATGGCACAAGATGCATATCTTTCTTTAAATGCTCAGGCAAGCTGGGGCATAAGCCTGATTCCACCAAACCTATATTTCTGCAGCCAGCCTCTCTGTCTTCTCTGGGATGTTGAGTAACTGTTCCCTTACAACTGGCAGCAGCTTTCAACGTTCAGCACTATGCACCTTTTTTAGACTGATTTTTTTGCTTACACTTTTAACTTTGTATTGTCTCTTCTCTTCAATAGACATTTGTTACCTGGTTTGTTTTAATACTAATTTTATACTAG
Seq C2 exon
GAGTTGGAAATCTGCAAAGATCATCCAGTCAGCGTAGCACACTCACATACCAAAGAAATAATTATGCTCTGAACACAACTGCTACCTATGCGGAACCCTACAGGTCAATGCAGTACCGACTGTCAGAGTCTGGCTATAACAGGCTGCAGCACACAGCGCCCGCTGATGATGGGACCACGCGATCTCCATCCATAGATAGCATCCAAAAGGACCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012561:ENSGALT00000020513:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.726 A=NA C2=0.685
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0051418=Arm=PU(9.8=5.5)
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:
GCCTGAGGAGTTCGTATGCTA
R:
TGTGCTGCAGCCTGTTATAGC
Band lengths:
345-1899
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]