DreINT0047626 @ danRer10
Intron Retention
Gene
ENSDARG00000089372 | clk4a
Description
CDC-like kinase 4a [Source:ZFIN;Acc:ZDB-GENE-030131-576]
Coordinates
chr14:6629541-6630004:-
Coord C1 exon
chr14:6629890-6630004
Coord A exon
chr14:6629708-6629889
Coord C2 exon
chr14:6629541-6629707
Length
182 bp
Sequences
Splice sites
5' ss Seq
ATAGTAAGT
5' ss Score
8.65
3' ss Seq
TTTTTTTTTTTCTTTCCCAGTGC
3' ss Score
11.3
Exon sequences
Seq C1 exon
TTGGAGCTCGCATTGCGCTGAAGATCATTAAAAATATTGAGCGCTATCGTGATGCGGCTCTATCTGAGGTTGAGGTGCTGGAGCAGATTAACTCGCTAGACTGTGACAGGCGATA
Seq A exon
GTAAGTGCCTCTGAAAGCAGCTAAAACAGTAATCTCCTACAATTTATGCCTCTCCGATGCATGGCGGTGTGATATCACACTTAATTTGAAATTTACAGCCTCTCAGGTGTAAAGAAGTCCAGACAGCGTATTAGCAGTGCCGTATTTCATCTGCTTTTTTTTTTTTTTTTTTTCTTTCCCAG
Seq C2 exon
TGCTTGTGTGCGGATGTACGACTGGTTTGATCACCACGGGCACATCTGCATTGCCTTTGAGCTGCTGGGCTTGAGCACGTATGATTTTCTGAAGGAAAATAACTTTCAGCCCTTCTATATCAACCACATCAGGCACATGGCCTACCAGATCATCAGAGCAGTCAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000089372:ENSDART00000162196:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PU(12.9=97.4)
A:
NA
C2:
PF0006920=Pkinase=FE(17.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGAGCGCTATCGTGATGCG
R:
TCTGACTGCTCTGATGATCTGGT
Band lengths:
246-428
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]