BtaINT0039375 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005408 | CLK1
Description
CDC-like kinase 1 [Source:HGNC Symbol;Acc:HGNC:2068]
Coordinates
chr2:89925092-89926403:-
Coord C1 exon
chr2:89926175-89926403
Coord A exon
chr2:89925183-89926174
Coord C2 exon
chr2:89925092-89925182
Length
992 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGA
5' ss Score
5.41
3' ss Seq
CGCGCACTTGACGTTTCCAGAAG
3' ss Score
5.69
Exon sequences
Seq C1 exon
CTATTACCTGGAAAGCAGATCCTTAAATGAGAAAGATTATCATAGTCGACGCTACATTGATGAATACAGAAATGACTACAGTCAAGGATGTGAACCTGGACATCGACATAAAGATTATGAAAGCAGATATCAGAACCATAGTAGCAAGTCCTCTGGTAGAAGTGGAAGAAGTAGTTATAAAAGCAAACACAGAATTCACGACAGCACTTCATATCATTGTTCACATGGG
Seq A exon
GTATGAGCTCTTTTAAATTTTTTGGAAATTTTATTTCCCATGTGGAACAGGAAAACTTGAAATTGTGTTTGATCATTTGAGAAAGTTCTATTTAAGATGAAGTCATCTCAGTTTTAACTTACAGGATTCTTTGTGCATTGGATAGGAAATTCCTGAAATACAGTACATGTTTAATTGTATGGTAACATTTTATTAATCATTGGCAACTAATTGTCATTCTTGTGAAATAGTGTAGATAATGTCTATTAGCTTATAGCAGGGATTACAAGATATTCTGAAAATATTTTTATGGTACTTTAAGAAATTTGATTTGCTTTGATAAATGAAAGTCTTATCTACAAGTATGGTTTTTATATTTGTATGATTGAGGATTATGCATTGCCTTTGTTCTGGCTAATCCTTTTATCACTAAAAAACAGATTTGAACATTATGGGTTGGTTATGTGTTAATTTGGAGCTCAAGCTCAGATGACATTTTAAATACTGTAGTGTTCTTGTATGCCAATTTTTTTTTCTCCCCAACATTAGAATTTTTATTTACTGTTTCGATATTTGTTTTCTTAGATTAGCTAGGAAATTATAATTTGGCCACAGTCTACTTTTGACAAGTAAATAATTACATTCTACAATTTTGCAACATTAAATTAGGACACTAGAAACTTAAGTTTTATGTTTCAGTGAATGCTACAACTAAGCATTTTTTTTTTTTTTTTAAGAAAAACAATTGTATTATGTTTTGTTACCTTGCCACTTTGAGTATCTTATCTGAAAATCTGTTCCTTGCCATGTTTTTCTCCTGTTAACATAAACTATGTGCCCTGTGAATTTCTGGGGACTGAATTTGAAATTGCTCCTGCCAACCGTTTGTGGCCTGGCGTGTATCTGAATGCCTGAATATCTCCCCGCTGAATGAATTTCGTATTCTGCCCTGAATTCACTCGGGTATATTGATTGGCTGGATGATCTTGGTGCCGCGCACTTGACGTTTCCAG
Seq C2 exon
AAGAGTCACCGAAGGAAAAGAACCAGGAGTGTAGAGGATGATGAGGAGGGTCACCTGATCTGTCAGAGTGGAGACGTACTAAGTGCAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005408:ENSBTAT00000007115:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.753 A=NA C2=0.484
Domain overlap (PFAM):
C1:
PF105774=UPF0560=FE(41.8=100)
A:
NA
C2:
PF105774=UPF0560=FE(16.5=100),PF0006920=Pkinase=PU(0.1=0.0)
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:
ATTACCTGGAAAGCAGATCCTT
R:
ATCTTGCACTTAGTACGTCTCCAC
Band lengths:
318-1310
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]