DreINT0114942 @ danRer10
Intron Retention
Gene
ENSDARG00000060184 | pkn1a
Description
protein kinase N1a [Source:ZFIN;Acc:ZDB-GENE-061207-17]
Coordinates
chr1:45138947-45139274:+
Coord C1 exon
chr1:45138947-45139023
Coord A exon
chr1:45139024-45139131
Coord C2 exon
chr1:45139132-45139274
Length
108 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
TTTTTGTCTCTTATTCTCAGGTA
3' ss Score
10.39
Exon sequences
Seq C1 exon
AGATCTTAAATTAGACAACTTGCTGCTTGACACAGAGGGTTATGTGAAGATTGCCGACTTTGGATTGTGTAAAGAAG
Seq A exon
GTAAAAGCCTCTTTTTGGACTTTGATTATTTCTTTGTTTTCCTTTATCACCCATCTGATGACGTTGTTGCTCATGTTGAATTGGGATGTTTTTGTCTCTTATTCTCAG
Seq C2 exon
GTATGGGTTTTGGGGACCGGACCAGTACGTTCTGCGGGACTCCAGAGTTTCTGGCTCCAGAGGTTTTGACAGACACATCGTACACCCGTGCTGTGGACTGGTGGGGTCTCGGAGTGCTTATATATGAAATGTTGGTGGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060184:ENSDART00000132555:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(10.0=100)
A:
NA
C2:
PF0006920=Pkinase=FE(18.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGATCTTAAATTAGACAACTTGCTGC
R:
CTCCCACCAACATTTCATATATAAGC
Band lengths:
218-326
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]