MmuINT0037403 @ mm9
Intron Retention
Gene
ENSMUSG00000026034 | Clk1
Description
CDC-like kinase 1 [Source:MGI Symbol;Acc:MGI:107403]
Coordinates
chr1:58476965-58478152:-
Coord C1 exon
chr1:58477927-58478152
Coord A exon
chr1:58477056-58477926
Coord C2 exon
chr1:58476965-58477055
Length
871 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGA
5' ss Score
5.41
3' ss Seq
CGCCCACTTGACGTGTCCAGAAG
3' ss Score
4.61
Exon sequences
Seq C1 exon
CTATTATCTGGAAAGCAGATCCATAAATGAGAAAGCTTATCATAGTCGACGCTATGTTGATGAATACAGGAATGACTACATGGGCTACGAGCCAGGGCATCCCTATGGAGAACCTGGAAGCAGATACCAGATGCATAGTAGCAAGTCCTCTGGTAGGAGTGGAAGAAGCAGTTACAAAAGTAAACACAGGAGTCGCCACCACACTTCGCAGCACCATTCACACGGG
Seq A exon
GTATGAGTGCCTTTTAAACGTTCTGAAAGGTTTTATTTCCCATGGAGAACAGGAAACAGTTTTGTGTTTGAGAAAATTTCAAGATAAAAGTCATCACAACTCTACCTTGCAGGAGTATTCTTTTAGTATTTGTGTATTACATAAGAAATTCATGAAAATAGTGATATTTAGTTCTGTAATGATAGGAAAGATTGTCTTAATGCTATTCCAAGAAATACTATTTTGATAAATTGTCAGTTTGTTCCAAGGAATTAGGTATTTTTGTGTTAGGGTTAGTTATGACTTATTAACATGTGTAAATTTTTTTCCTCATTAAGTTACAGATTTGAAGTTAGTGTTTTCATGTATTAATTTGGAAATCTATCAGATAACATTTTAAATGTTATAGTGTTATATACCTTTTTTTTCCCTTCCCAAATTAGGGCTATCATTTTATTTACTATTTTAATATATATTTTCTTTATTAGTTAGGCCAAATCTTAATTTGGCCACAGGGTACTAAAGTAAATACTACATTCTACAGTTTTGTAGTATGAATTTAGGACACTATGTTTGAGTGAATGCCACAGATAAGTTTTGTTTTGTTTTTTAAGAAGAAAAGCAAATGTGTTTATGTTTTGTTGACTTACCACTTTGAGTATCTTATCTGAAAATCTGTTCCTTGCCATGTTTTTCTCCTGTTAACATAAACTATGTGCCCTGTGAATTTCTGGGGACTGAATTTGAAATTGCTCCTGCCAACCGTTTGTGGCCTGGCGTGTATCTGAATATCTCCCCGCTGAATGAATTTCGTATTCTGCCCTGAATTCACTCGGGTGTATTGATTGGCTGGATGATGTTGGTGCTGGTGCCGCCCACTTGACGTGTCCAG
Seq C2 exon
AAGAGTCACCGAAGGAAAAGATCGAGGAGTGTAGAGGATGATGAGGAGGGTCACCTGATCTGTCAGAGTGGAGACGTACTAAGTGCAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026034-Clk1:NM_001042634:3
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.829 A=NA C2=0.484
Domain overlap (PFAM):
C1:
PF105774=UPF0560=FE(42.4=100)
A:
NA
C2:
PF105774=UPF0560=FE(16.9=100),PF0006920=Pkinase=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGGAAAGCAGATCCATAAATGAGA
R:
TCTTGCACTTAGTACGTCTCCAC
Band lengths:
310-1181
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: