DreINT0114943 @ danRer10
Intron Retention
Gene
ENSDARG00000060184 | pkn1a
Description
protein kinase N1a [Source:ZFIN;Acc:ZDB-GENE-061207-17]
Coordinates
chr1:45139132-45139464:+
Coord C1 exon
chr1:45139132-45139274
Coord A exon
chr1:45139275-45139356
Coord C2 exon
chr1:45139357-45139464
Length
82 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
ATCTGAAACTGTCTTGCCAGTCC
3' ss Score
4.62
Exon sequences
Seq C1 exon
GTATGGGTTTTGGGGACCGGACCAGTACGTTCTGCGGGACTCCAGAGTTTCTGGCTCCAGAGGTTTTGACAGACACATCGTACACCCGTGCTGTGGACTGGTGGGGTCTCGGAGTGCTTATATATGAAATGTTGGTGGGAGAG
Seq A exon
GTGAGCTTGTTTTAGGCTTTTAGATATGAAATACTCTTTCAGAATCGTGAGAGATGTGTCTGATCTGAAACTGTCTTGCCAG
Seq C2 exon
TCCCCATTCCCAGGTGATGACGAAGAGGAAGTTTTTGACAGCATAGTGAATGATGAAGTTCGATACCCCAGGTTCCTGTCCGCAGAGGCCATTGGCATCATGAGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060184:ENSDART00000132555:19
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
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCTCCAGAGGTTTTGACAG
R:
AGGAACCTGGGGTATCGAACT
Band lengths:
169-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]