HsaINT0036423 @ hg19
Intron Retention
Gene
ENSG00000013441 | CLK1
Description
CDC-like kinase 1 [Source:HGNC Symbol;Acc:2068]
Coordinates
chr2:201724848-201726189:-
Coord C1 exon
chr2:201725961-201726189
Coord A exon
chr2:201724939-201725960
Coord C2 exon
chr2:201724848-201724938
Length
1022 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGA
5' ss Score
5.41
3' ss Seq
CGCCCACTTGACGTTTCCAGAAG
3' ss Score
6.57
Exon sequences
Seq C1 exon
CCATTATTTGGAAAGCAGGTCTATAAATGAGAAAGATTATCATAGTCGACGCTACATTGATGAGTACAGAAATGACTACACTCAAGGATGTGAACCTGGACATCGCCAAAGAGACCATGAAAGCCGGTATCAGAACCATAGTAGCAAGTCTTCTGGTAGAAGTGGAAGAAGTAGTTATAAAAGCAAACACAGGATTCACCACAGTACTTCACATCGTCGTTCACATGGG
Seq A exon
GTATGAACGTTTTTAAAACATTTTGGAAATTTTATATCCCATGTGGAACAGGGAAACTTGAATTTTTGTGTTTGATTATTTGAGAAAGTTTTAAGATGAAATCATCTCAGTTTTAACCTGCAGGATTTTTTCTGTGTTTGTGCATTGGATAGGAAATTCCGGAAATAAAGTACACATTTAGTTCTATAATTTAATTATTGGTTGGCTCCTAATTGACATTCCAGTGAAATGATGGGAGTTAATTGATTTAATTTAGATTAGTTGAAAATTATTACAAAATATTCTAAAAGGGTTTTTTGTGGTACTTCAAGAAACCTGATTAGTTTTGATCTATTGAAATCACAAAAGTAGAACAGGGCATTTTATTTTTGTATAATTTAGGATTAGGTATGCTTCTTTGTTCTAACAAGTCATGTTTTCTAACCCTTCTTTCACTAAGCAAACCAGAACAGATTTGAACTGTTATGGGTTATATATTAGTATGGAGATCAGCTCAGATGACATTAAAAATGCCGTAGTGTTATTCTTGTATGCCAAATCTTTTTTTCCCCAAAATTAGCACTTTAATTTTATTTACTGTTATAATATTTGTTTTCTTAGATTAGGTAGGAAATCTTAATTTGGCCACCGCCTACTTTGACAAGTAAATATTACATCATACGATTTTGCAACATTAAATTAGAACACTAGAAACTAAAAAATTATGTTTCAGTGAATGCTACAACTAAGCATTTTTTTTTTTTAAGAAAAACAATTGTATTATGTTTTGTTGCCTTGCCACTTTGAGTATCTTATCTGAAAATCTGTTCCTTGCCATGTTTTTCTCCTGTTAACATAAACTATGTGCCCTGTGAATTTCTGGGGACTGAATTTGAAATTGCTCCTGCCAACCGTTTGTGGCCTGGCGTGTATCTGAATGCCTGAATATCTCCCCGCTGAATGAATTTCGTATTCTGCCCTGAATTCACTCGGGTATATTGATTGGCTGGATGATCTTGGTGCCGCCCACTTGACGTTTCCAG
Seq C2 exon
AAGAGTCACCGAAGGAAAAGAACCAGGAGTGTAGAGGATGATGAGGAGGGTCACCTGATCTGTCAGAGTGGAGACGTACTAAGTGCAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000013441-CLK1:NM_001162407:3
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.795 A=NA C2=0.484
Domain overlap (PFAM):
C1:
PF105774=UPF0560=FE(42.5=100)
A:
NA
C2:
PF105774=UPF0560=FE(16.8=100),PF0006920=Pkinase=PU(0.1=0.0)
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:
TGGAAAGCAGGTCTATAAATGAGA
R:
TCTTGCACTTAGTACGTCTCCAC
Band lengths:
311-1333
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)