DreINT0047605 @ danRer10
Intron Retention
Gene
ENSDARG00000062954 | clk2a
Description
CDC-like kinase 2a [Source:ZFIN;Acc:ZDB-GENE-030131-298]
Coordinates
chr19:9248108-9250300:+
Coord C1 exon
chr19:9248108-9248198
Coord A exon
chr19:9248199-9249462
Coord C2 exon
chr19:9249463-9250300
Length
1264 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAAT
5' ss Score
6.15
3' ss Seq
TCCTCTTTTTTTTTTCTCAGCGA
3' ss Score
9.71
Exon sequences
Seq C1 exon
GAAACAGAAGTACTTTTATCGTGGACGCCTGGACTGGGATGAGAACTCTTCAGCAGGAAGATACGTCAGAGAAAACTGCAAACCTTTACGG
Seq A exon
GTAAATTTGTTGGCTTCATATTTAAATCACCTATAGCTAAATGTGCAATTTTACAAGGAATATATATATATATATATATATTGGTCTTGTAATACTCGAGGCTCAATTGATTTGATTGAAATACACTAAAATAGTTAGAAATTGTATTCTTTATTCCAGTTTAAACTTACAGAAATATATCTGTTATATTGTAACATGCTAGTTAGGTGTTAATTGGTTGTCAATAGTTATTGTTCTTATTATGGGAAGTTTAGTGAACAGCATTTATGAACCTGAATCATTATACAATTAGTTACTATTACTTTTGATTGAACAAGTTTGAATTTCTATTTAAAAAAAAAACAACAACTTTTAAATTATGATTTTTTTTTCCAGCACATCTATAAATACATTTTTTCAAGTAAATGCAGACTTAGTAAGCATAATAGACATGGCCTTTAAAATGACTTTAAAACGAGCCAATAAACTAATCACATTTTATTGACAGTAAAATGATAGTTTTGAGAGTCGAGAGGTGCCATTTTACCAGCTTTGCCAAGAACGCACAGTAGCACAATGGCAAGCAACAGGAGCAAGTATACTATGTAGAAATATGTGCTTATGTCTATGGAATTATTGCACACGCAAGCTAGTCAACGGTGCAGTGAATATGGCTTTTTTGGCTCCTATATTCGCTGTTATTCTCACTTGGCCGGAAACCAAAAATTGCCATTTACTACCAATAATTTTCAATGGCCAAACATTTAGTGTATCCCTAATTTATCATTCGTTAATTACATTATCTTAAGAGTTATTAACACATGTAAATGACTGTAGTTGACCTGGAAATGTAATGGTTAATCCACTGTAATAGTAAACAGTGGATAAAAAAATGTGTTGTTGACTTTATATTTGAATATGATCAGATCTAATAACTGATTTTTTTTTTTTTTAATCTTTGCCATGATGGCAGCACATAATATTTCCCTAGATATTTTTCAAGACACTAGTATTCAGCTTAATGTGACGTTTAAAGGCTTAACTAGGTTCATTAGGCAAGTCTTGTATAACATTGGTTTGTTCAGTAGACAATACTAACCTTAACCTTTTTAAACCAGACTTTCTCCAGAAGAAAAAATATGAAAGAAATTACTGTGAAAATGTCCTTAATTCCTTAAGTTTCACTAGAGAAATATTCAAAAAAGAATAAATATTGCACAGCAGGGCTCATAGTTTTGCCCTCAACTGTACTGATCGTCATCCTCTCCTCTTTTTTTTTTCTCAG
Seq C2 exon
CGATATCTTCTGTCTGAAGCTGAGGAGCATCACCAGCTGTTCGACCTGATCGAGGCCATGCTGGAGTACGAGCCATCGAAGCGTCTGACTCTTGCTGCAGCTCTCAGGCATCCGTTTTTCCAGAGCGGCATCAGCAGCAGCGAACTGAGCGCAGGTAAGAGCTGGGAGGCAAACCGTGACATCAGCCGGTGACACTGACACTCTCGTCTTCAACCAACGCCAAAAAAAAGGACTCGCATGCCGACAGGATTACATGGAGCTGGACTGACGTTCGTTTTGTAGAGCAAGAGATAATAAAGCCATGAGTTTTCTGTCATCCTTCCATAATGTGAGGACAGCTCCATGTCAGCAATGAAAATGTGAAGAAGATCCCAGAAAACAGTCATGACTGATTGGACAATGGGGAATGGGAATGAGTTTCAGTTCTTCCAGCCAATTTGGCCAATTTTTGGACTTCCACAAGTGGTGTGATGGTCAAAAGCATTAACTTAACACTCCATTTTTGAAAATAACTGACGAAATGAGTATCGCTGTTACAGCTGAGGGGGATACGTTTTGCGCATTTTTAGCGATCAGCTGAAAATCAAAAATGCGACAACGTTTGTATTCAGTTCACTTCAAACCAAGTAAGCGAGAGCAAGAGCGTCCCTCAGCACACGTTTACAGTATTTATTTAGATAAATAGCATCTCTTTTTTTGTGTCTTTGTATGGATCCGATTGTATAAATATGTGTAAATATGAATAAATATATGTTGTGACTATAGAATAAAGGGGCTGTCTGTGTGCTTGCTGTGAATGGGTTTTCACAGCGGTTCTACAGGCAAAATGTTTTTACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062954:ENSDART00000142910:11
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=FE(9.5=100)
A:
NA
C2:
PF0006920=Pkinase=PD(12.3=60.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTTTATCGTGGACGCCTGG
R:
GAACGTCAGTCCAGCTCCATG
Band lengths:
353-1617
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]