BtaINT0039378 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005408 | CLK1
Description
CDC-like kinase 1 [Source:HGNC Symbol;Acc:HGNC:2068]
Coordinates
chr2:89923167-89923539:-
Coord C1 exon
chr2:89923423-89923539
Coord A exon
chr2:89923334-89923422
Coord C2 exon
chr2:89923167-89923333
Length
89 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGT
5' ss Score
8.54
3' ss Seq
GTTTTTTCCTATGTTTATAGCCG
3' ss Score
7.23
Exon sequences
Seq C1 exon
GGGAGGTAGACATGTAGCAGTAAAAATAGTTAAAAATGTGGATAGATATTGTGAAGCAGCTCGCTCAGAAATACAAGTTCTGGAACACTTAAATACAACAGACCCTAGCAGTACATT
Seq A exon
GTAAGTATCAAAATAGAACTTAGGAAATGGCCTCAGGTGGATTGGAATTGTGAGAGGCTGAACTCAGTTGTTTTTTCCTATGTTTATAG
Seq C2 exon
CCGCTGTGTCCAGATGTTGGAGTGGTTTGAGCATCATGGTCATGTCTGCATTGTGTTTGAACTATTGGGACTTAGTACTTATGACTTTATTAAGGAAAATGGTTTTCTGCCCTTTCGACTGGATCATATCAGGAGGATGGCATACCAGATATGCAAGTCTGTGAACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005408:ENSBTAT00000007115:6
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:
PF105774=UPF0560=PD(2.2=10.0),PF0006920=Pkinase=FE(12.3=100)
A:
NA
C2:
PF0006920=Pkinase=FE(17.7=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:
GCAGCTCGCTCAGAAATACAA
R:
AGTCGAAAGGGCAGAAAACCA
Band lengths:
182-271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]