BtaINT0039399 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007304 | CLK3
Description
Bos taurus CDC-like kinase 3 (CLK3), mRNA. [Source:RefSeq mRNA;Acc:NM_001034248]
Coordinates
chr21:34445498-34447649:-
Coord C1 exon
chr21:34447433-34447649
Coord A exon
chr21:34445595-34447432
Coord C2 exon
chr21:34445498-34445594
Length
1838 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TCGGGGGGCGGTGCATGCAGAGA
3' ss Score
-0.12
Exon sequences
Seq C1 exon
CCATGACCGCTTGCCCTACCAGAGGAGATACCGGGAGCACCGTGACAGCGACACATACCGGTGTGAAGACCGGAGCCCATCCTTTGGGGAGGACTACTACGGATCTTCACGTTGCCATCATCGTCGGCGATCACGGGAGAGGGAGCCATACCGGACCCGCAAGCACGCCCACCACTGCCACAAACGCCGCACCAGGTCTTGTAGCAGCGCCTCCTCG
Seq A exon
GTGAGTGGTGGCCGAGTGTGCTGGCTGGGGCTTGAGGGCCTCGTCTCTTTCTAGCCTTCTCTCAGGTGGCTGGTCTGGGTGAGTACTGCCAGCCATACGCACGCGCATTTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTTGTCTGGTCCAGTTGCAGGGCTGAGCAGGGGCCCAGCTCCTCTGTCTTCTGGCCCACTGGCAATGGAAACTTAGGGGTTCTGGTTCCGGCGCTGGCTGGCCTCTGGCCTCCCTGTCTCCACACTGCTCCAGGCACAGGCCATGTGTGTGAGTGGCCAGGGACACTTCTTCAGAATCCTTAATAGGGTTGCTGGTATGTGGTCTAGAGCTGTTTGACCTGGTCCTTCCCACCCAGAGATTGCCCCACCACACAGCTGAGTGGTCTGACTGGTGTGGACTGTATCCACCTCTGCAGTCTCCTCTCTACACCCCTCACCAGAAGGCCTGGAGGCTGGAGCGCCCATGGGTGGGGGGCGGGGTCCGTCCGTCAATGAACTTGGACTGGGACCTGCCCTCTGACCTTCAGGCACGCCCTCTTCAGTCTAGCCTCTTCATGTGAGGGGCAGTCAAGGCGAGGGGGATGAGCTGCCTGTGGGGTGGGGCATGCGAAGAAATGGCAGAAAGGCCCCCAGCTCCAGGCCGTGTCCAGTTGAAGGTCACATGGCCAGAGCAGGGCCTGGAAGCATTCTTCTTTCGGAGTGTTGTACAGATCTCTGCTGAGACCAGGAACCTGCTCTGTGCTCAGCTCTCTGGGAAGGAAGGCCAGTTGTGTGTCTCGGAGGGTACATGCTGTCTTGTCTTCCCTTCCCAGCCCTCTGCCCTCCCTCCATGGCTCCGGGCCGCGAGGCCCCAGGGAGCAGTGGTGCTGCAGTGGAGGGGCCAGGTGTCTTTCTGCCGAGCTTTCCCGTGACTTCTCTGAGTGGCCGTGAGTTGAGGGTTGACCGGGCACACGGCATGGCCTGGTGCCCTCTCTGCACACTGCCACAGGCGTGTGGCTCTGCTTCTTCTCTTTTTGGTGCCCTTTGTTGTCATGAGGCTCAGGTTGGGTCTGGCCTGTGAATCGCCTCAGTGCCAAGGCCAGGGCAGGAGCTGGCTTGGGGCCTGTGTGGGCCGTTGTGGTGGTAGGCCTTGGAGAGTTGACCGGCCCAGAGGATCCAGCGCTCCTTCTCTGCTCGAGGCTGGTGGTGCAAGGGCTGCCGATGGAAGGCTGGTTCTGCTGGTGATGCTGAGTCTGGCCACAGATGCTGTCTAGGGGCAGGTGGCAGCTGTCGGGCATGTGCAGGACCGCGTGGGTAGACAGACTGGGCATTCTGCAGCTGAACCAGAGTGGCCTCTGACCGTTCTGGATGATCTGACTGAGGCTCGGCCCGCCGTCTTCTTGTACCGTTCTCACTGCGTCTTCACCTTGGCTGAAGCCGAAACGGGAGGGCCGGGAGGGGGAGACTCAGTGGAGGAGGGAGTCAGGCCTGCGACTCTCCACGTGGCCCAGCCCCTTAGCTGCAGAGGCTGGGCATCTTTCTGAGCATTTGCGGCGCCTTTCTTTTAGATAATGTCCGAGTTTTCTTTACATACCTGTAGCTGTTTTTACTTTTCTGTTTTGAAGTCAGTTTGTGTCTTGACGTGTCCCTTGCAATATCCCTATCGTTATATATGCTGTGTGCCTTATGAAATGCTGGGATCTGGAAAATCCAATCAACCAACCCACCGGCTCCTCACCGTCTCCACCTCTGCCTTTGACTGACACCTCAATCTGTCAATCGGAACCGCCTACCATGCGATTGGTCGGATGGCGTTTCGGGGGGCGGTGCATGCAG
Seq C2 exon
AGAAGCCAACAGAGCAGTAAGCGCAGCAGCCGGAGTGTGGAAGATGACAAGGAGGGCCACCTGGTGTGCCGGATCGGCGATTGGCTCCAAGAGCGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007304:ENSBTAT00000009609:3
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=0.424
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
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:
CCATGACCGCTTGCCCTAC
R:
CTCTTGGAGCCAATCGCCGAT
Band lengths:
310-2148
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]