MmuINT1007288 @ mm10
Intron Retention
Gene
ENSMUSG00000026034 | Clk1
Description
CDC-like kinase 1 [Source:MGI Symbol;Acc:MGI:107403]
Coordinates
chr1:58420121-58421308:-
Coord C1 exon
chr1:58421083-58421308
Coord A exon
chr1:58420212-58421082
Coord C2 exon
chr1:58420121-58420211
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:ENSMUST00000034868:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.785 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
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types