GgaINT0124748 @ galGal3
Intron Retention
Gene
ENSGALG00000004689 | PKN3
Description
NA
Coordinates
chr17:5849147-5850091:+
Coord C1 exon
chr17:5849147-5849429
Coord A exon
chr17:5849430-5849936
Coord C2 exon
chr17:5849937-5850091
Length
507 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
TTATGACATAGTTTGTAGAGATG
3' ss Score
-10.75
Exon sequences
Seq C1 exon
GGCAGCTGTCTCTTGCAGCTGGGCAATGGTGTGAACTTAATGGATCCAAGCTTCCAGCAAAAACTGGAGGGCGAGAAGGAACTACTTCGTCGTGCTATACAGAAAGAACTGAAAATTAAAGAGGGAGCAGAAAACCTGCGTAAAGCGACGACAGACAGAAAAAATCTTGCTCATATAGAGCATGTGCTGAAATCCTCCAACCGCAAACTAGAACAACTTCATTGGGAACTTCAGGAGCTCAATGCAAGGATTGTGATAACTGACAAAGAGGACAATAAGACAG
Seq A exon
GTATGGCATAGGTCACAGACAACAGGAAAATCTTACGGTGCTCCAATGCTAGTGGGGATTTTACCTGTTGGTATTCAGCTGATGAAATAATCTGTGCGTTAAAAGGTTGGGAATGGAGGCAATTGAGGTGAAAGGAGTCAGGTAACATGAGAGATTAGTGTAGAGGGAAGAATGCTGGGCATGAACAATATTCAGGAGCAGGCTGTAGGTGAAATTGAAGGGATCTGAGTAGAGTTTCTAGGCAGCTGAACATTTAAGTACCTTATGGGATGTGAATGAGTGTAAAATTGAAAGAGTGATAGGTAGGAGTGGTTCACTGATAAAAAGAAATACTTATAAACTTAAGCTTCATTTGAAACAATATTTTGCTGTCAGTTTTGTAGAGAATAGAGACCTTTCTATGTGTTATTTTGGAGCTTAACCTTCTTTTGTGGAATCATTTTGAACCACACAGTGGAATAACCCAAGAAGAGATGACTAATTATGTTTATGACATAGTTTGTAGAG
Seq C2 exon
ATGGATCTTTATCTCCTGACCCCTGTCTCTGGGAAAGAAACCCAGATCCCATGGCAAGGAAGATTGAAGCTCTGAAAAAGCAGCTGCATGTTGAAATGAAAGTCAAGCAAGGTGCTGAGAATATGATCCAGATGTATTCAAGTGCAACATCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004689:ENSGALT00000007470:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.274 A=NA C2=0.442
Domain overlap (PFAM):
C1:
PF0218511=HR1=WD(100=70.5)
A:
NA
C2:
PF154561=Uds1=PU(50.6=76.9),PF0218511=HR1=PU(44.4=61.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGGGCAATGGTGTGAACTT
R:
TGCAGCTGCTTTTTCAGAGCT
Band lengths:
354-861
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]