DreINT0115014 @ danRer10
Intron Retention
Gene
ENSDARG00000079585 | pkn3
Description
protein kinase N3 [Source:ZFIN;Acc:ZDB-GENE-030131-1902]
Coordinates
chr5:31241437-31243262:-
Coord C1 exon
chr5:31243080-31243262
Coord A exon
chr5:31241547-31243079
Coord C2 exon
chr5:31241437-31241546
Length
1533 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
TCATTTTTTTTGTCTCTCAGCTG
3' ss Score
9.3
Exon sequences
Seq C1 exon
GGCGATTGGAGGTCAGGTTGATGGGTTGTCAGGACCTGCTGGAGTCAGTTCCAGGCCGCTGTCGTGTAAGCAACATGTCCTCCGCTCCTGGAAGTCCATCTGACTCCAAATCACTAAGAATGAGAACCGGCCTTTCCACTCGCAGCACCAACGGCAAGACCACCAAGACTGATGAACTGTCAT
Seq A exon
GTGAGTTTCTCACGGGCAGCAGGGTGAAAAATAATAGATTTCATAATAATAGTTAAAAAAAAAAACTGTTGAAAACTTTTATTTTGTTGTCCAAATACATTTTTAAAATGGATAAAACAAATGTTACTGCAGTAATTATTATAAAGCCATTCAATTTATCTTTTTTTTATTCACATGCACTTTTTTTTTTTCTAATCAAAATAACTAGGGGTGTAACCGATCACAGTTGATCTGTGATTCGTACAGAACACAACCCACAGTTTGGAACACAAGTGGCCCTCGGATTAATACTTTTTTTTTTTTTTTTACTTCAATTTAGATTAATCTTGAATTTGTAACTTTCACAGATGCAGATCTCCTCTTGAGTCATTTACATCAAATGTATGAAAGAATTTATGCTTTCCTGTAAAATATAATGATGACAGAAGGTGGGTTATTCGGAATGTGGTGGGTGTCATTAAAAGTGTTTTTCTGTTACTAGTTTAGCCTGCATTAATGTATTCAGTGTAAGCCATTTGAATAATCATCAAACGATTAGGATCTCAACACCCAAGCAACATAAATGATAAATGATGATGATTTGCATACAGTTATTAATTCTTCGAATCGCTGCATTCAAATCTGAAACCGTAAAAATCCAAAAAGAGATTCAGTCTTTAGTGTTTTGAGTTGGTTAGTTAGTTACAAATGCTCAAATAACACAGCAGTACTAGGATAGCATTTTATAGTTTAGATAAAACCACTGATGTTTATGGTAAAGATCAAAATCATCTTCATATGCATCTAATGATGCTCAAAAATGAAAGTTGTTTGCAGCATTTACATTATTTACCTAATATCAAAACCAGTCATCAAAAATATGCCACTGAATAATTCTTCAAAAATGATCCATCCAGCAATGAAACGTGAAGTTTTATGAGTGAATAACTGAATCATTTATTGACAATGAGACTAATAAAAAATTGGAATTGTTCAAACTATATTGTTAGAAATTTTTTTTTTATTAGCTGATTATTTCTTCATTATATTTTTAATAAAATTACAGGTTCCAAGTTCTGTTTGTTGAAACCAAAAGTTTCCTGCAGTGCTGCTTTTGTAATAAATGGAAAGCAAATTACATTTCACTCCAATGTGAGATTTTGTGATCGGTTACACCACTAAAAACAACTAACCACTTGAAAAAATATCTCTTCTGTGAAATTTGAAAGTGGTTAAATCTCAGTATGTTACAGATCCTGTTTACACCTGAACTTATCATAGCCCACTTATGACCAAGTTACCAAAAGTGTATTATATAAACAAGGGCCTAAATTATAGTAATAGCTTTATTAAGCAATATTCAACTTTTTCAATCAAGAAGCACTGAGATGCGCATCACAGAAAATACCTTCACAAATGATGTTTTTTTTTTATGTCTTTTGATTGATTTTATTTTTACTTTGTTCTTGGGAATCAAACAATTTTATGGAAATAGTTTTGAAAAAAATTCAAGTGGTTTTATAAGTATGATGCTTCATTTTTTTTGTCTCTCAG
Seq C2 exon
CTGAAATCAGTGCTGTGTTGAAAGTGGATAACAAGATTGTTGGTCGCACACATTGGCGGCCGCTGAGTAAGGATGCCTGGAACCAAAGCTTTAGCATCGAACTGGAGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079585:ENSDART00000112546:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.613 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAGGTCAGGTTGATGGGTT
R:
CCGCTCCAGTTCGATGCTAAA
Band lengths:
287-1820
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]