MmuINT0037445 @ mm10
Intron Retention
Gene
ENSMUSG00000020385 | Clk4
Description
CDC like kinase 4 [Source:MGI Symbol;Acc:MGI:1098551]
Coordinates
chr11:51276118-51277935:+
Coord C1 exon
chr11:51276118-51276247
Coord A exon
chr11:51276248-51277852
Coord C2 exon
chr11:51277853-51277935
Length
1605 bp
Sequences
Splice sites
5' ss Seq
TGGGTTAGT
5' ss Score
3.1
3' ss Seq
CCTGTGTTTGTTTTGAATAGCTC
3' ss Score
7.9
Exon sequences
Seq C1 exon
AAACGAGATGAGCGCACATTGAAAAACACAGATATCAAAGTTGTTGATTTTGGAAGTGCAACATATGACGACGAACATCATAGTACTTTGGTGTCCACAAGGCACTACAGGGCTCCAGAGGTCATTTTGG
Seq A exon
GTTAGTAGTCACCAGACTTCTTATCCTTTTAATTGTTGAAGGTCATGGTTAACTAAAATGATGTTAGGAGGATACAGAGAAGAGTTATGCGTGTTTCTCCTGTATGACCATGTTTGTGAAAGATATTCTGAGTGCTGATGATATGTGATTTTTAGCTGATTATAACATGGTGGGTGTGCTTGGTGAGAGTATCATAGTCTCGTGATGGGGAAGTTATGTTGCCATCTGTTTTCGCTCCACTGCCAAGGTAAGGCTCTGGTACACATGGCCAAGGGCTTGGTTGGCTAACCTAGACATGAAATAGACATGGAGCAGGACGAAAGGAAGGAACTTGTAAGCAAGAGAGTCTCTGTGTTAGCCATGGTGGGAGAAAGCTGGAAGTGAAAGGTAGAATTTTTGAACTCAGGGAACATGTGTTATACCTCAAAACTTAGAAGTCACTGGTAGGATTGGTGGCTTGGAAACAAGACAGATCGGGTGCTATTATTGATACAAATCTGAAGTTGGAGTCACTGGAAAAGGAATCTGGAGACTGGGGGAATAGAATACTATTTGTGTGGGTGAAGTTCCCTAGGATGAAGGCAGATTAGAAAGGAAGATGTAGTTGATGTAGTTGAATGCCACAGTTGCTTTAGACATTGGTGGTCAGGTAATGTTGGGAAAGGGTGAGAAAAGTGAGATGAGGTTCCAGAGTATCAGAAGTAGTTCACTCTGGAGAGATGGCTCAGCGGTTAAGAGCACTGACTGCTCTTCCAGAGGACATGAGTTCAATTCCCAACAACTACATGGTGGCTCACAACCATCTGTGACGGGATCCAACACCCTCTTCTGGTGTTTCTGAAGATAGTGACAGTGTACTGAGTACTCACATACATACATACATACATACATATATACATATATACATACATACATACATACATACATACATACATACAAGAGAAAGAGAGAGAGAGAGAAAGAAAAAGAAAGAAAGGAAAGGAAGGAAAAGGAAAGAGAAGAGTAGTAGTTTGCTGAGGAATGAAGGGCTGCAGTTAACCCCCTGAGGAAAAGTATATTGAGGTGTAGTGATTGAAGAAGAAAACGTTTATCTAAGCCCAAGCTCCACTGCTGCAGATGGAAATGTATTTGCTATATAAGTTTTCCAATGATGAGCATTGTAGAATGAACAAAAGTGACTAAATCAGGGCCAGCACCAGCCTATAATTCTGCCACTTAAAAGACTGAAGAAATGCCATGTTCTTGACCAGCCTGAGCTACACGCACTAAAGTTATAAATCCTGAGGTTGCTGATGTGGTCTCTGAGATACACTATGAAGAGTACCTGCATGTAGGGAAGGGTGAGCAGTTTAAAGCTGTTGGCTGGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCGAAGGTCTGAAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCACCCGTAATGAGATCTGATGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATCTTTAAAAAAAAAAAAAAAAAAAATAAAGCTGTTGGCTATAACTTGCCTGTGTTTGTTTTGAATAG
Seq C2 exon
CTCTAGGTTGGTCTCAGCCTTGTGATGTTTGGAGCATAGGCTGCATTCTTATTGAGTACTACCTTGGGTTCACAGTCTTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020385:ENSMUST00000093132:9
Average complexity
IR
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(13.6=100)
A:
NA
C2:
PF0006920=Pkinase=FE(8.5=100)
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:
ACGAGATGAGCGCACATTGAA
R:
TGAAAGACTGTGAACCCAAGGT
Band lengths:
210-1815
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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