HsaINT0036440 @ hg19
Intron Retention
Gene
ENSG00000176444 | CLK2
Description
CDC-like kinase 2 [Source:HGNC Symbol;Acc:2069]
Coordinates
chr1:155236520-155237917:-
Coord C1 exon
chr1:155237801-155237917
Coord A exon
chr1:155236687-155237800
Coord C2 exon
chr1:155236520-155236686
Length
1114 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGC
5' ss Score
6.95
3' ss Seq
TCCCCCATCTCTCTTCTCAGCCT
3' ss Score
8.55
Exon sequences
Seq C1 exon
GGGTGGGGCTCGAGTTGCCCTGAAGATCATTAAGAATGTGGAGAAGTACAAGGAAGCAGCTCGACTTGAGATCAACGTGCTAGAGAAAATCAATGAGAAAGACCCTGACAACAAGAA
Seq A exon
GTAAGCAAGCAAGGAAGTATGTAGGGAGGCTGAGAGCCCCAACCCCTACACGGGAGAGACTTCTAGACCTGGTTTAGGCAGACAGGGGAGTCCTAGACCTTCTCATCCATTCATCTTTTGTTCATCATCTTAGAGTAGTAGAACATCAGGGTAGGAAAGGGGGGGGGCCCATGACATTCCTTAATCCACTCCCCTTGTTTTCAGGGAAGTTAGATTGCTCTGTCGTTTGACCCCAGCCTAGAATGGCTTCTGTAGAGATATACCCTGGACATAGCCCTAGGACTGAGCATCAACCTCATCGAACAATGAATTAAGCTTTTATAAGTAGAACTATGCTGATAAGGCCACAGACATTTATGCAGTAATATTTTGTTCACATACATTCACAGTCCAAAAATAGAATAAGGACTTTAAGCCAAGATATGAGGCCAGTAGGTATAAATAGGAGCCCAGTGGTAGCTAGTGGTGAATGAATATCAGGAGTTGGGCTGGGGTTGGGATTTAGGATGGACAGTTTGATGATTCAGGATCTATACTGTTTGGAGCTTGGCACTCCACAGCTCTTCAGCAAATAGTTTTTGAACTATTTAAAATGACGCAGGAAGATATTTTGAAACTTGGGCTGGGCATGGTGGCTCACGCCTGTAATCCCAGCACTTTGGAGGCCGAGGCGGGTGGATCACAATGTCAGGAGTTCGAGACCAGCCTGGCCAATATGGTGAAACCCCGTCTGTACTAAAAATAAAAAAATTAGCCGGGCATGGTGGTGGACAACTGTAGTCCCAGCTACTTGGAAGGCTGAGGCAGGAGAATCGCTTGAACAGGAGGCAGAGGTTGCAGTGAGCCAAGATCGCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACGCCATCTCAAAAACAAAAAAGAAAAAAACCTGGCAGATAGTACCATTCTTCTTGGGTCTGGTAGAGGCTACTCCTTAGCTGAACTGAATTTTGGTGTTAGTACTAGCTGGCATGGTTTTACACAAGTATGTGGAATCAACAGCTATGAAGTACCTCCTTGTTGGATGGCTGATGGGCAGATGGGAGCTCATCAGACAACCCCCCTTCCCCCATCTCTCTTCTCAG
Seq C2 exon
CCTCTGTGTCCAGATGTTTGACTGGTTTGACTACCATGGCCACATGTGTATCTCCTTTGAGCTTCTGGGCCTTAGCACCTTCGATTTCCTCAAAGACAACAACTACCTGCCCTACCCCATCCACCAAGTGCGCCACATGGCCTTCCAGCTGTGCCAGGCTGTCAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000176444-CLK2:NM_003993:6
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(12.3=100)
A:
NA
C2:
PF0006920=Pkinase=FE(17.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTCGAGTTGCCCTGAAGAT
R:
ACTTGACAGCCTGGCACA
Band lengths:
278-1392
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)