HsaINT0036462 @ hg19
Intron Retention
Gene
ENSG00000113240 | CLK4
Description
CDC-like kinase 4 [Source:HGNC Symbol;Acc:13659]
Coordinates
chr5:178044345-178045779:-
Coord C1 exon
chr5:178045557-178045779
Coord A exon
chr5:178044436-178045556
Coord C2 exon
chr5:178044345-178044435
Length
1121 bp
Sequences
Splice sites
5' ss Seq
TCGGTATGA
5' ss Score
7.72
3' ss Seq
CTGCCCACTTGCCGTTCCAGAAG
3' ss Score
7.46
Exon sequences
Seq C1 exon
TCATTATTTAGAAGCAAGGTCCTTGAATGAGCGAGATTATCGGGACCGGAGATACGTTGACGAATACAGGAATGACTACTGTGAAGGATATGTTCCTAGACATTATCACAGAGACATTGAAAGCGGGTATCGAATCCACTGCAGTAAATCTTCAGTCCGCAGCAGGAGAAGCAGTCCTAAAAGGAAGCGCAATAGACACTGTTCAAGTCATCAGTCACGTTCG
Seq A exon
GTATGATTGGTTTTGTTTTCAATTTGAGTGGAGTTTTATTTGTGTGTACTCTTAACGAGCTGATAAGTTTCTAATTTTTTATATATATATATATAAAATACTATTTGGATATATTATAATTGTATTTATATTACTTAAATCCTTAAAGGAAACCTCCAAATTCTTGTAGCTGATCTGTATATTTATTAGCTAGCCCTCATTTGCCCACATTTCCTCATATTCTGCAGACCAGATAATGAGTTTATTGATTTTAATAATAAAACTATTTTTTTATTTGTAACATATTCTTATGAAAAAATCATGCACCCATATCTTTTCTTTCATCTTAAGCATTTTTTTTTTCTTAGAAACCCTTTATCTGGTACTTGAAAATAAATGTGAAATATTGCACTGGTGGACACCTGAATGTTACTAACCTGCATAGAGCATAGTTCCATAGTCCAGTGCATCATTGTCTGCAATGAATTCTTTTGAAGTTGTGAAAATGGGTGCTGAATGGGAAACATCCAAAAAGTCTGCCCCCCCCTTTTTTTTTTTAACACTCAGACATCTTCACCTGCTTGAACAGTGAACTTTGAATTAGTTTCTCCCCAAGTTTTCTTCAGTAAAACTAGTTTTTATTAGATTGAACATTGAAATTAACTAGCCTTTATTTTCCCCTTTTATTTTAATCATGTATATTTTAAAATATTGCTAAATTAGAATAATTTCAAATAGTCTTGACATTTTAAAACATTTTTCTGAAAAACTAGACATCTCAATTCACAGCATATGCTGTTTATAGCAAGAGATAAGTAAATCATGACATTGCATTCTTTAAATTTCAGACTTCAATTAAATCAGTATTTTAAAGAGACAATTGTGTTGTTTTTTTCTATTGCCACTTTAAGTATCTTATCTGAAAATCTGTTCCTTGCCATGTTTTTCTTCTGTAACATAAACTGTGCCCTGTGAATTTCTGGGGACTGAATTTGAAATTGCTCCTGCCAACTGTTCGTGGCCTGGTGCTTATCTGAATGCCTGAATATCTCCCCGCTGAATGAATTGCGTATTCTGCCCTGAATTCACTCTGATATATTGATTGGCTGGACGATCTTGGTGCTGCCCACTTGCCGTTCCAG
Seq C2 exon
AAGAGCCACCGAAGGAAAAGATCCAGGAGTATAGAGGATGATGAGGAGGGTCACCTGATCTGTCAAAGTGGAGACGTTCTAAGAGCAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000113240-CLK4:NM_020666:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.329 A=NA C2=0.323
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
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:
TCATTATTTAGAAGCAAGGTCCTTGA
R:
TGCTCTTAGAACGTCTCCACT
Band lengths:
310-1431
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)