HsaINT0036427 @ hg19
Intron Retention
Gene
ENSG00000013441 | CLK1
Description
CDC-like kinase 1 [Source:HGNC Symbol;Acc:2068]
Coordinates
chr2:201721614-201722607:-
Coord C1 exon
chr2:201722441-201722607
Coord A exon
chr2:201721709-201722440
Coord C2 exon
chr2:201721614-201721708
Length
732 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGT
5' ss Score
8.54
3' ss Seq
AACTTTCTCTTTATTCTCAGTTT
3' ss Score
7.61
Exon sequences
Seq C1 exon
CCGCTGTGTCCAGATGTTGGAATGGTTTGAGCATCATGGTCACATTTGCATTGTTTTTGAACTATTGGGACTTAGTACTTACGACTTCATTAAAGAAAATGGTTTTCTACCATTTCGACTGGATCATATCAGAAAGATGGCATATCAGATATGCAAGTCTGTGAATT
Seq A exon
GTAAGTTCTTGGTATATCTTCGTTAATTTGCTGGTTTTATCCATTCCACATATCAAAATGTGCATCCTAAGTGTGTACAATTTTTATTTGATTAAAAATAAAGGGGGAGGAAGAATAGGTATGAAGAGATTTGATTACAGGCTGTTGATCCAGCAGTGTACATTTCATTCAGCAAGTAGGATATCCACCATATAACAACGTACTTTGTTGCAGACTATGATTTAGACTTTTCTGATGCGCAAAAATAGTAACTTCGAATGCTGGGTAAAAATTAAGGCGTGATATATCTCATAAAAGAAAGCTTCATAAGAGGTAGTAAGTTTTAGTTACTGGTGATTTTCTAGCAGACTGGAATGTTGACCATTCTTTGGGAAAGGAATCAGAGGTTTTTTGTTGGGTTTTTTTGTTTTTTGAAATGGAGTCTCGCTTTGTTGTTCAGGCTGAAGTGCAGTGGCGCAGTCTTCACTCACTGCAAACTCTGCCTCCCCAGTTCAAGTGATTCTCCTGCCTCAGCCTCCCGAGTAGCTAGGACTACAGGCACACGCCACCACACCCGGCCAATTTTTGTAATTTTGGTAGAGACAGGGTTTCACCATATTGGTCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATTACAGGCGTGAGCCACTGCACCCGGCCTGTTGTGGGGTTTTGTGATTTGGTTTGGTTTGGTGTTTTCTGATTACAGCAACTTTCTCTTTATTCTCAG
Seq C2 exon
TTTTGCACAGTAATAAGTTGACTCACACAGACTTAAAGCCTGAAAACATCTTATTTGTGCAGTCTGACTACACAGAGGCGTATAATCCCAAAATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000013441-CLK1:NM_001162407:7
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(17.7=100)
A:
NA
C2:
PF0006920=Pkinase=FE(15.9=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:
CCGCTGTGTCCAGATGTTG
R:
TATTTTGGGATTATACGCCTCTGTGT
Band lengths:
262-994
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)