RnoINT0037365 @ rn6
Intron Retention
Gene
ENSRNOG00000025768 | Clk1
Description
CDC-like kinase 1 [Source:RGD Symbol;Acc:1311469]
Coordinates
chr9:65305842-65307995:-
Coord C1 exon
chr9:65307863-65307995
Coord A exon
chr9:65306003-65307862
Coord C2 exon
chr9:65305842-65306002
Length
1860 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GTAAAAATTGTCTTTTATAGATG
3' ss Score
7.77
Exon sequences
Seq C1 exon
CCAGTTTTCGGACAAGAATCTCTTGCTGGTGTTGTTCGCACCATTTTGTGCTGAGAGGTAGTTGCTGCCGCTTGCACACTTCCCTCCGTCGCCTTGAGAGCTTTGTCTTCAGGGTTGGAGTCTCTGCGGAAAG
Seq A exon
GTAAGACGCGGTTTCTGTCAGGGCCCTTCCTCCTATCCCGGCGCTGTCCGGCTGTCTCCTTGGGCCCGCTGCCTCCTCGGACCCCGCCGCAGCTCTTCCTGTCGCAGCCATGCGAAGGGGCTCTGCCTCGACTGTAGAGCTCTGGCCGCCAGCTTCTGTGTATGTGGGGACGGTGCCGGCAGGCTCCGCGTCCCAGGAGGGCGGGCCCGCTGCCAGCGCCTCAGCGACCGCGGTCAGACCTAAGATGGCGGTAGGGGGAAGGCCGCGTTCGTCCTTCCGAATGGCGGCGCCGGGCGCGGCCTTCGCTTAAACTCGATCAGTACTGGTTTTAATCTCGGTGGTGGCTCGGCGCAGTTTTTGGTGCTGATTTTCTTTATATTTGAAGCGAAAGGTCTTGTTAACCAGGCCGGACCCACACGCCGAGGTGATCTTGTTTGGGGTGGGCGCTGCAGGGTCAGCTTCACAGCAGGCTGTCACCCCAGTTCTGAGTAGAAGCCTTCGCCATGACAAAACCCGGCTTCGACGAAGAATTTCAGAAGCAGTCAGTCAACACGAAAGCAAAATCGAGCATATTGAAAATAGATGGCACACCGGGACAGGGCTTATCAGAGCGAGGAACGAGTGCTTTTTAGGAAGAGTTTAGGATTTAGTTAGGTATCTAGAGGTTGTGAAATCCTCTTTGTTTTAAACAGGGTTCAAAGGGTGTACTTTGTAACAACATTAAAATTCAAGAAGGCGGAGCTGTGGTGTCGCACACCTTTAATCCCGCACTGGGAAGACAGGCAGGCAGATCTCAGAGTTCGAGGACAGCCAGGGCTACACAGAGAAAGCCTGTCTTTAAAAAAAAAAAAGTTAAAGACAATTTCCTTTGTCAGCCACCTTGTGGGTGCTGGGAATTGAACTCAGGACCTCTAGAAGAGCAGTCAGTGCTCTTAACGGCCAAACCATTTCTTCAACCCCTGACAATTTCCTTTGTAAATAAAGTTGTAAAGTGGCAGTTGTTTACCTTCAGGAAACAGGAGGGGAACACCCTAAGAGTATGTCACTTCCGCACTCAGTAAACCGCCCTATTTTCATCCTCCTGGCCTGCCCTGTGAAGTAGATTGGCTTTATTGGCGGCGGTGCCCGGATTTTGCCGACTCAGATCCGCGGGCACCCATGATGAGCTGTTTTCCTTTTCAGGCTTTCCTCCCATATTTTCATGATTTTCCTCGTCTCCCTTTGCTAGCAGTAAGGGTATCTGCAGGGACTGTGGAAATTTTCGTGAAGGAGCATTGGGAAGTCAGGTCATATGCTGACCAACTTTTTTCTTTTTTTCTTTTTTTTTTGAGTTGTAAACAAGCACATAACATCCAAACATTTTAAAAACTTCTTAATTAGGGTCAATTATGGTTATGTTGGGTGTAGACTTAGTTTGGGTAGAAATTGGATTTCCTGAACCTGTAATTTGAATTTCTGAAAGGGCTGTCATATGTTTTGCTTAAGTTATATAGAAACTCTTTCCACTTACAAATTTGGGCATGGTGAGAACAAGGTAAGGTAAAGTTCAGATTGCAAATTCTGAGGCATTGAAATAATATTTATGATTTTAGGCAGTTGACTACAATTTTAGAACCTTTTGTTTGATTTAAAACAAAAGGTCAGTGCTGGGGGTGACATGGATTTAATCCCAGTACTCCAGAGGCAAGAGGCAGGTAGTTCTCTGAGTTCAAAGGCAGCCTGGTCTACATAGCTAGAGCTACATATACATAGTGAGACCATCTGGGAAGGGGGAAAGATCAAAACTAGTGGGAATTTGCAGAGTTTTACTACTGCACATCACAGAAATACAATTTAACTGGTAAAAATTGTCTTTTATAG
Seq C2 exon
ATGAGACATTCAAAGAGAACTTACTGTCCTGACTGGGATGAAAGAGATTGGGATTATGGAACATGGAGAAGCAGCAGCAGTCATAAAAGAAGGAAGAGATCACATAGCAGTGCCCGTGATTATAAGCGATGCAAATACAATCACTCCAAAACAACGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025768:ENSRNOT00000030934:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.333
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF105774=UPF0560=PU(26.3=85.2)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGTTTTCGGACAAGAATCTCT
R:
CTGTCCGTTGTTTTGGAGTGA
Band lengths:
294-2154
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]