DreINT0115006 @ danRer10
Intron Retention
Gene
ENSDARG00000079585 | pkn3
Description
protein kinase N3 [Source:ZFIN;Acc:ZDB-GENE-030131-1902]
Coordinates
chr5:31230759-31232465:-
Coord C1 exon
chr5:31232323-31232465
Coord A exon
chr5:31230867-31232322
Coord C2 exon
chr5:31230759-31230866
Length
1456 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
3' ss Seq
TATCCTCTTATGGCCGCCAGTCT
3' ss Score
3.8
Exon sequences
Seq C1 exon
GTATGGGATATGGAGATCGTACATCAACCTTTTGTGGCACCCCAGAGTTTCTGGCTCCAGAGGTTTTGACAGACAGCAATTACACCCGTGCAGTGGACTGGTGGGGTCTGGGTGTGCTCATCTATGAGATGCTCGTTGGAGAG
Seq A exon
GTCAGTCTTGCTGCTCAGACTCTTACTACAGCAGCATCACTGTAAGACCCCGCTTATACAGAAATGGACAAAATTGTTGGTACCCTTCAATTTACTCCAGACCAGCTTTATTAGTTAGCCTTTTATAAACTTCGGTTGAACCACAATTCCAAAGCAATATCTCATGTTGTTTCTCTCCCTTCAGTGAAAAGGTATCAACAATTTTGCCCGTTTCTATATGCTATCATGATCTGTGTTTTTGGCAATCTAATCACAAGTGGGTGGCACTTCTTACCCCTCTCTTTCAGCTCCCCACACTTACCTGTTGATACTTTCTACTGTCCTGTCTATTAAAAGGTGTTTGTGAACCTATTTTTTATATAAAAAAAAATTTGTTATAAAATTTTAGACTTGTGCAAGGCTAAATACTTTGGATTTTTTTTTCGAATATCCCAGTTTGAAAAGATTTTCATATGACCTATCAAATTTTATTAAAAATTTAATGCGTTTAATAATACAATAATAGTTTTGTTTGAATTTGTTTTATTAATTATCAAGTATATTTATTCACAAACACTATAACCCTTACCAAGAATAGAAGAAAAAATCGCTGTCAATTACTTCAATTTACAATAATAATAATTTAATTAAAAAAAAATGTAGGCCAGGTCAGTATCCTCAGCAGTAAATAAATGGAGAACTTTTAAGCAAATGTTGCTTTAAGGTCAGTAATTAAATGCTATTTTAAAATAAAGTTTTAATGAGATGGATTGTTGGTGATTGTACATTGCTTTATTTGCACATCTTTTATGCGATAATCTAGTCTTGTGCATGAAGTTAATTAGCATTTTTTGGATGGAAACATAGCTACTGCATTGCAACTGAAATCTGCAGAAAGGTAGTCATGTCTGTTATAAAATTGCATAAATTTTCTGGATACATTTTCATAATGCATATTTTTCATATAAAAAAACTAATAATTTTATTAATTTTTTATTAAAAACAAATTTTTTTATTTAAAAAAAAAAATAAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAAAAACATCAATACAGATCAATATTTTAAGACTGTTTTTTTTTTGTAAACATGAAAATGTAAACCGATGTTTTAGTATACTGTTAACATGCTTCTCTCTTTGAAATGCTCTATGAATTTATGTTTTACGTTTTTACTGCAAATGTCACATCCATAACTCTAGAATTGCTCTTCAATATAAGCCAATAATAAATTAAGCAAGTTTGAGATCTGAAATGGGTAATGTAATGGGTTATTGCACTATAAAAACATCCTGTATGTCAAAACATCAAGAGAGTTTTGATCTCCGTTCAAAAGCAAACAAACAGAAAAGGCAACCCCACACTTTTGAACAGTAGTGTTTGTGTGTATCCTCTTATGGCCGCCAG
Seq C2 exon
TCTCCATTCCCTGGTGATGATGAAGAGGAGGTGTTTGACAGCATAGTGAATGATGAAGTGCGCTACCCCAGGTTTATGTCTCCAGAGTCAGTCTCCGTTATCCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079585:ENSDART00000112546:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.028
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(18.1=100)
A:
NA
C2:
PF0006920=Pkinase=FE(13.5=100)
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:
TGGGATATGGAGATCGTACATCA
R:
TTTGGATAACGGAGACTGACTCT
Band lengths:
246-1702
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]