DreINT0047640 @ danRer10
Intron Retention
Gene
ENSDARG00000005908 | clk4b
Description
CDC-like kinase 4b [Source:ZFIN;Acc:ZDB-GENE-050227-19]
Coordinates
chr21:32251355-32251774:-
Coord C1 exon
chr21:32251708-32251774
Coord A exon
chr21:32251472-32251707
Coord C2 exon
chr21:32251355-32251471
Length
236 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
ATGTGATTTTAATATTTCAGAGG
3' ss Score
6.87
Exon sequences
Seq C1 exon
ATGAGATTGTAGGGACTCTGGGAGAAGGAGCCTTTGGAAAAGTCGTGGAGTGCCTTGACCACACAAA
Seq A exon
GTAAGTCAGATTCTGTGGCTTTTTTTATGAAAAAGAGTTGTTAACATTAAGAAAGTTTTAATTGGGTATTATAATTAATTAGGTTTATCATTGTTTTGGATGCATCAGTGGTGGTAGTTTCTAAGGCAACCATTTTGATTCAGACATAAATTAGCATTGTAAACAATGCGCAAATGAAGCCTAAAAGTATTATTTCTTAGAAATCCCTAATGCTTAATGTGATTTTAATATTTCAG
Seq C2 exon
AGGTAATGTAAGAGTGGCACTGAAAATCATCAAAAATATTGAGCGCTACCGTGAGGCAGCATTGTCAGAAGTTGATGTGCTTGAGCGGATAAACTCTCTCGATGATGAAAAGAGATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005908:ENSDART00000139890:5
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=PU(6.9=95.7)
A:
NA
C2:
PF0006920=Pkinase=FE(12.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGATTGTAGGGACTCTGGGA
R:
GAGAGTTTATCCGCTCAAGCACA
Band lengths:
164-400
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]