RnoINT0037406 @ rn6
Intron Retention
Gene
ENSRNOG00000003714 | Clk4
Description
CDC-like kinase 4 [Source:RGD Symbol;Acc:1310274]
Coordinates
chr10:36727130-36728853:+
Coord C1 exon
chr10:36727130-36727196
Coord A exon
chr10:36727197-36728736
Coord C2 exon
chr10:36728737-36728853
Length
1540 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGT
5' ss Score
8.31
3' ss Seq
CATCATCTTTTGTTTTCAAGGGA
3' ss Score
8.18
Exon sequences
Seq C1 exon
ATGAAATCGTGGACACTTTAGGTGAAGGGGCCTTTGGCAAAGTTGTAGAGTGCATTGATCATGGCAT
Seq A exon
GTAAGTTTGCTTTTTCCTTTTTGAACATTCTGCTATATTTTACAATGTACTTAAAGTGGTTGCTACAAGTTTTCCTGAGAGAAATTCAACAGAATTTCTGAAATGCAATGTAATGTATGTGCCATGAGTATTAGTTTTATTGTGAATGGTGGCAGTTTTTCTCAGGTGGAAGTTACTCTGTAAAGGAATGCTCAAACAAGATATGTAGCATTCTGGTACTTTTGAATTGCAACATCAATAAAATACATCTAAATTTACATGTTAAAGTACATCTCCTGAACTACAGATTCTATTAAGACCTATAGAATAAAGTCTATATTCTCTGGTAAGATACATTGACTTTACCTACCTATTTGTACCACCTCCCTTCAGAACCTCTGCTCTGTAGTTTTACTACTTTTTGTAAGTGAATGTAAAAACTTAATTGAAACTACACATTTCTAAAATGATATCTATTTTTTTTTCATCAGAAATAGTTAGAAAGGGTATAAGTTTACTGTATATATATCAGTAGTTTTAAAAGTAAGGTTTGTCTTTAAACATATTTGGTGAGACTTACTATCATAGCTCCTTGATCTGTTTTCCAGAAACTGAGTTCACACTTGGAAATGTGTTTTTATCCCCATATTTGGAAATGTTTTATTGTTGAGCTTGGTTGTGGCTTAGTGGTACAGCATTTGCCTAGCAAGGTGCTTTTTCAGTCACTAGCCAAAAAAAAAAAAAAAAGTTTTAGCCCTTAATTTACTTTCATACCATTTTCTATGATTTTCTCAAAACACTGAGTTTATACTTTTTGGAGTGTTCCTGGAAATGCCTCAACCCAAGCCCACTGCCCTCAATGTAGCTATTACTCCATACTTGGATACAATGGGCCTGTAAAGTGCTGGGGTAGGGAGAGCTTCATAACTTGTAGGCGGGGTCTTTGCCCAGCTGTTTGATTTCTTTCACAGCTATCTTTCAGGCCCAGTTCTGTATTGTTGTGTAAATTGCTACTTTACTGAATGAATATCTGGAGCTTCATCTCTTTGTCATTGAACTGAGGCATAAAGGAGTAGGTCCTGTCGTTCTGTACTAGCTCCTGTGCCTTGTCTCTAGCACAGAATAGGTCCAGCCTGGTAAATGAACACAGTGCTTTGAACAGCAGCATACTCTGATTCTTAGCACACTGGAGCATGTGCGTGCGTGCGTTACTTTTAAATGTTTTGTATAAAATCTAGATAAAATTTTAGAAGCATGTTAAAATTTCTAAATATTACATGGATGGTTGCTTTGTTTTGAAAAGATGATCTGGTACCTAATATGGGCTCTGAAAGGTTAGAGCAAGTGTATGGGAACTTGTAATTACAGTTGTATTTTAGGAAGCTGAGGTAGGAGGAGCACAAGCTCAGTGTCAGTCTGGGCTACATAATGAGTTGAAGCACAGCCTGAGCAAGCTACTGAAATCTTGTCTCTAAAACAAAACAAAGAATGTTCTTTTCACAGAGGATGCAGTTTCATCCCACCTCTTGTACATTTAGCATCATCATCTTTTGTTTTCAAG
Seq C2 exon
GGATGGCTTACATGTGGCAGTGAAAATTGTAAAAAATGTAGGCCGTTACCGGGAGGCAGCTCGCTCTGAAATCCAAGTGCTGGAGCACTTGAACAGCACTGACCCCAATAGTGTCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003714:ENSRNOT00000005048:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PU(0.1=0.0)
A:
NA
C2:
PF0006920=Pkinase=PU(13.2=97.5)
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:
TGAAATCGTGGACACTTTAGGT
R:
AGACACTATTGGGGTCAGTGCT
Band lengths:
182-1722
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]