HsaINT0036429 @ hg19
Intron Retention
Gene
ENSG00000013441 | CLK1
Description
CDC-like kinase 1 [Source:HGNC Symbol;Acc:2068]
Coordinates
chr2:201719727-201721534:-
Coord C1 exon
chr2:201721405-201721534
Coord A exon
chr2:201719810-201721404
Coord C2 exon
chr2:201719727-201719809
Length
1595 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
AATTTTGCTTTGCTTTGCAGCCC
3' ss Score
8.91
Exon sequences
Seq C1 exon
AAACGTGATGAACGCACCTTAATAAATCCAGATATTAAAGTTGTAGACTTTGGTAGTGCAACATATGATGACGAACATCACAGTACATTGGTATCTACAAGACATTATAGAGCACCTGAAGTTATTTTAG
Seq A exon
GTGAGTATTAATTGTCCTTTGAGAACCTTTGTATTTCCTTATTGAGACTTAAAATTTTTTTAGCAGTTTTAGGTCTTACTTGTGGGGCTTTATCATATTCTCTTTAAGGGATAAGTATCATGAAGTGCATTATGGATTTTAAGCTCTCAATTGTACCAGATAATTAGCTCTGGGAATTTGAGCAAGTGGCTTAACCTTTCTGGAATTGTTTTCACATTTGTAATATGTGGTAGGGTTTTTAAATGTAATTGTTTAATGCCAGGTGGGGCGCGGTGGCTCACATCTGTAATCTCAGCACTTTGGGAGGCCAAGGGTGGGGCGCGGTGGCTCACATCTGTAATCCCAGCACTTTGGGAGGCCAAGGCGGGCAGACCACATGGTCAGGAAATCGAGACCATCCTGGCTAATATGGTGAAACCCCATCTCTACTAAAAATACAAAAAATTAGCTGGGTGTGGTGGTACACGTCAGTAGTTCCAGCTACTCAGGAGGCTGAGGCAGAATTGCTTGAACACCGGGAGGCGGAGGTTGCAGTGAGCCAAGATTGCGCCACTGCACTCCGGCCTGGGCGACAGAGCGAGACTCCATCTCAGAAAATTGTTTAATGCCTATTTTATTCCAGACTATATATAACACTATATAATTTATTTATTTTTATCATTTATTTATTTTTTAGACGGAGACTTACTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCAATCTTGGCTCACTGCAACTTCTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTATAGGCACCCACCACCACACCCGGTTAATTTTCTTATTTTTGGTAGAGATGGGGTTTTTACCATGTTGGCAGGCTGGTCTCAAACTGCTGACCTGGAGCAATCTGCCTGCCTTGGCTTTGCAAAGTGCTGGGATTACAGGCATAAGCCACTGCGCCCGGCCATATATATTGTATTTAACCTTGGATTAAGTGATTGCTTTAGGATCTTCCAGCTCAAACATCACATTGCATATATATGTGTATATATATAATTTTTTGGGGGGGGGGCGGAGTCTTGCTCTGTCACCCAGGCTAGAGTGCAGTGGCGCGATCTCGGCTCACCGCAAGCTCCGCCTATGGGGTTCACTCCATTGTCCCACCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGCCTGCCACCATGCCTGGCTAATTTTGTTTTTGTATTTTTAGTAGAGACGGAGTTTCACCGTGTAGTCAGGATGGTCTTGATCTCCTGCCCTCGTGTTCCACCTGCCTCAGCCTCCCAAAGGGCTGGGATTATGCCTGTAGCGTGAGCCACTGTGCCCGGCCAATTCAGATATATATATATCTTAATAGAGGTGGGATCTCGCTGTGTTGCCCAGGCTGGTCTTGAACTCCTGAGCTCAAGCAGTTCTCCCATCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGTGCCCAGCCTACATTACATGTGTTTTTTTTTTTAAAGTATTAGTGTTAACTAACTTTTTAATTTCTTTAACAAACATTGAGTATTTTTTTTCCTTAAATTTTGCTTTGCTTTGCAG
Seq C2 exon
CCCTAGGGTGGTCCCAACCATGTGATGTCTGGAGCATAGGATGCATTCTTATTGAATACTATCTTGGGTTTACCGTATTTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000013441-CLK1:NM_001162407:9
Average complexity
IR-S
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(13.6=100)
A:
NA
C2:
PF0006920=Pkinase=FE(8.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGATGAACGCACCTTAATAA
R:
TGGAAATACGGTAAACCCAAGA
Band lengths:
210-1805
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)