DreINT0114937 @ danRer10
Intron Retention
Gene
ENSDARG00000060184 | pkn1a
Description
protein kinase N1a [Source:ZFIN;Acc:ZDB-GENE-061207-17]
Coordinates
chr1:45136465-45136720:+
Coord C1 exon
chr1:45136465-45136538
Coord A exon
chr1:45136539-45136644
Coord C2 exon
chr1:45136645-45136720
Length
106 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCG
5' ss Score
10.05
3' ss Seq
GTGTGTGTGTGTGTGTGTAGTAA
3' ss Score
6.31
Exon sequences
Seq C1 exon
GAGAGGCAGCCGTCCACCGAGCCTCTCTCTGCTCCAGACGTCACCACGCCTATCAGAACACACTCATTGAGCAG
Seq A exon
GTACCGTCAAACACATAACTCCCACTATATCTAAGGTATTTTTGTGTTTTTTAAGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAG
Seq C2 exon
TAAACAGAAGAAGACTTCTCTGAGCCTGCAGGATTTCCGACTAATTGCAGTTCTTGGCAGAGGCCATTTTGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060184:ENSDART00000132555:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.960 A=NA C2=0.077
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006920=Pkinase=PU(5.0=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAGGCAGCCGTCCACC
R:
CTTTCCAAAATGGCCTCTGC
Band lengths:
150-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]