DreINT0047609 @ danRer10
Intron Retention
Gene
ENSDARG00000062954 | clk2a
Description
CDC-like kinase 2a [Source:ZFIN;Acc:ZDB-GENE-030131-298]
Coordinates
chr19:9242070-9242478:+
Coord C1 exon
chr19:9242070-9242186
Coord A exon
chr19:9242187-9242311
Coord C2 exon
chr19:9242312-9242478
Length
125 bp
Sequences
Splice sites
5' ss Seq
TAAGTGAGC
5' ss Score
3.93
3' ss Seq
GTTTTTCTTGTTTTTTTTAGTCT
3' ss Score
9.3
Exon sequences
Seq C1 exon
GGGTGGAGCACATGTCGCTCTGAAGATCATCAAAAATGTGGAGAAGTACAAAGAGGCTGCCCGCCTGGAGATCAACGTACTGGAAAGAATCAACGAAAAGGATCCTGAGAATAATAA
Seq A exon
GTGAGCTTCTTTGCATAATTACCACGTCTCGGCATGTTTTGAACCATTGCATGCCGCCTTGTTGGTGTGAAGTTCAAGATGGACCTAATAAACTGATTACTTGATGTTTTTCTTGTTTTTTTTAG
Seq C2 exon
TCTGTGTGTGCAGATGTTTGACTGGTTTGATTACCATGGCCATATGTGCATCAGTTTCGAACTCTTGGCTCTCAGCACTTTTGATTTCCTCAAAGAAAACAACTACCTGCCGTACTCCATCAACCAAGTCCGTCATATGGCCTACCAGGTCTGCCTGGCTGTCAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062954:ENSDART00000142910:5
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=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(12.3=100)
A:
NA
C2:
PF0006920=Pkinase=FE(17.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGCACATGTCGCTCTGAAG
R:
AGGCCATATGACGGACTTGGT
Band lengths:
256-381
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]