GgaINT0047234 @ galGal3
Intron Retention
Gene
ENSGALG00000012561 | PKP4
Description
NA
Coordinates
chr7:38048625-38050587:+
Coord C1 exon
chr7:38048625-38048816
Coord A exon
chr7:38048817-38050370
Coord C2 exon
chr7:38050371-38050587
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:ENSGALT00000037713:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.715 A=NA C2=0.687
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0051418=Arm=PU(12.2=6.8)
Main Inclusion Isoform:
NA
Other Inclusion 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]