BtaINT0039397 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007304 | CLK3
Description
Bos taurus CDC-like kinase 3 (CLK3), mRNA. [Source:RefSeq mRNA;Acc:NM_001034248]
Coordinates
chr21:34438146-34439372:-
Coord C1 exon
chr21:34439282-34439372
Coord A exon
chr21:34438638-34439281
Coord C2 exon
chr21:34438146-34438637
Length
644 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
CACTTTGTGTCCCTGAGCAGAGT
3' ss Score
6.29
Exon sequences
Seq C1 exon
GAAGCAGAAATATTTCTACAAAGGGGGCCTGGTTTGGGATGAGAACAGTTCTGACGGCCGGTATGTGAAGGAGAACTGCAAACCTCTGAAG
Seq A exon
GTCAGTTTCTGGCTTCCCCCAGCTCAACTCATGCCAAGGAGACCCCAGGCCTTGGGCAAATACACAGCAGAGGCCAGGCAGCTAACAGTGGCCTCCTCGCCCCAGCTCTGTGGGAGCCTGTGCCCAAGGCTGCCGGGTGCTGGCAGTGAGGCTTCTTGCAAACTGCCCTAGAGGGGCCCTTAGCTCTTCCCCTTCCCCACAGGGTGGCTCTGATGTACTCAGGGGGCATCCGAAGAGCCAGATATCTGAGACCCTGCTACTTCCCGCTCCCTCTTTTCTCACTAGGCAGGACTGAGGGGAGGGTGGGGGAAGACCTAGACATGGCCAGGAAGCCTCTGTCAACTGCATTTGGTGCTTGGACAAGTGAATTTCACAGAGGTGCTGTGTACCCACCTGTCAGAAGTTTGCACATGGGGGCAGAGGCATCAAGCCAGCAAGCCACCTGGTAGCCTGACAAAGTTCAGAGCAGACATGATTACAGGCACGAAAAGCAGACCTGTTCCTTGTCCAGGAGGGCAGAAGTAGTCCTCCAGGGGGGCATCCTGCCTCCTCAGCCATGCAGCAAGGCTTCCCAGAGGCAAGGGGACCGGCTGTGGCTTCCCATGGCCCGCCATCACACTGAGGCACTTTGTGTCCCTGAGCAG
Seq C2 exon
AGTTATATGCTCCAAGACACTCTGGAGCACGTGCAGCTGTTTGACCTGATGAGGAGGATGTTAGAATTTGACCCTGCCCAGCGCATCACACTGGCGGAGGCCCTGCTGCACCCCTTCTTTGCTGGTCTGACCCCTGAGGAGCGGTCCTTCCACACCAGCCGCAACCCAAGCAGATGACAGGCGTGCGGCCACTGCACCGGAGATGGAGAGCGGGACTGGGCTGCCCGGCCCCTTTCCTCCAACCTCTACCACCGGCCCCAGGGCCAGAGCCACGCAGTGAACAGTGCAATGTGAAGGAAGGCAGGAGCCTGCAGGGGAGGAGACCTGATGCCCAGCTGCCAGAAAGCACAGATTTGACCCAAGCTATTTATATGTTGTAAAGTTATAATAAAGTGTTTCTTACTGTTTGTAACCCCTGGTACCAGTGTGTCCATCTCCAGGCTCCTTGCCTTCTCCCCTCCCTACTTTATTAATAAAGTCTTTCTTAGCGGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007304:ENSBTAT00000009609:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.155
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(9.5=100)
A:
NA
C2:
PF0006920=Pkinase=PD(12.3=66.1)
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:
GGCCTGGTTTGGGATGAGAAC
R:
CATTGCACTGTTCACTGCGTG
Band lengths:
357-1001
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]