MmuINT0037441 @ mm9
Intron Retention
Gene
ENSMUSG00000020385 | Clk4
Description
CDC like kinase 4 [Source:MGI Symbol;Acc:MGI:1098551]
Coordinates
chr11:51087062-51088829:+
Coord C1 exon
chr11:51087062-51087128
Coord A exon
chr11:51087129-51088712
Coord C2 exon
chr11:51088713-51088829
Length
1584 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGT
5' ss Score
8.31
3' ss Seq
CATCATCTTTTGTTTTCAAGGGA
3' ss Score
8.18
Exon sequences
Seq C1 exon
ATGAAATCGTGGACACTTTAGGTGAAGGAGCCTTTGGCAAAGTTGTAGAGTGCATTGATCACGGCAT
Seq A exon
GTAAGTTTGCTTTTTCCGTTTTGAACATTCTGCTCTATTTTACAATGTATTTTAAGTGCTTGCTACAAGTTTTCTTGAGAGGTATTCAACAGAATTTCTGAAGCTCAATGTAATGTATGTGCTATGAGTATTAATTTTGTTGGAAATGGTGGCAGTTTCTCTCAGGTGGAGGTCATTCTGTAATTAAAGTAAAGCTCAAGCAGGTTCTGTGGCACTCAGCTGCTTTTGGGTTGCAGCATCGATAAAACACATCTAAACTTACACACTAGTGCCTTTGCTGAAGACCTACAGAATACAGTCTGTGTTCTCTGCTAAGATATACTGACCTACCTCACTGCACCATGTCTCATCAGAACCTCTGCTCTGTGGTGTTACACTTTTTGTAAGTGATCTTAAAAACTGAATTGAAACTACACATTTCTGAAATGACATCTAATTGTTTTCATCAGAAATAGTTGGAAAGGATATCATTTGTTAGCTTACTGTATATCAGGAGTTTTGGACATAAAGTTTGTCTTTAAACATATTTGGTGACTCTTAATATCATAGCTCCTTGATCTGTTATCCACAAAATGTTTGAATTCACACTTGGAAATATGGTTTTACCCCCATATTTGGAAATGTTTTATTGTTGAGCTTAGTGCTACAGCATGTGCAAGGTGCTGTTTCAATCCTTAGCCACAAAAACATTTTAGCCCTAAATTTACTTTTATACCATTTCCATGATTTTTCTCAAAATACTGAGTTTATACTTTTTAGGAGTATCCCTGGAAATGCCCCAACCCAAAACCTGCTGTCCTGGATGTAGCTATTTCTCCATACTTGGATAAAGCGAGCCTGTACTTGGATAAAGTGAGCCTGTAAAGTGCTGGGTAGGGAGAGCTTCATAACTTGTAGGTGGTGTCTTTATCCAGCTGTTTGATTCCTTTCACAGCTTGACAGGCTCACACCAATCTTTCAGGACCCATTCTGTATTGTTATGTAAATTGCTACTTTATTGAGTGAATATTTGGAGCTTCATCTCTTTGTGAGACTGTCTTAATGTCCTCATCTGTCTTTGTCATTGAACTGAGGCATAGAGGAGTAGGTTCAGTTGTTTAGTACTAGCTCCTGTCCTTGTCTGTAGCACAGAATAGGTCCAACCTAGTAAATGAACAAATGCTTTGAACAGCAGCATACTCTGATTCTTAGCATGCACGCACTCAAACTCGAGTGTATGTGTTCTACTTTTAAATGTTTTGTATAAAATCTAGATAAAATTTTAGAAACAAATGTTAAAATTTCTAAGTATTTCATGGATGGTTGCTTTGTTTTGGAAAGATGATCTGGAACCTAATATTATGGGCTCTAAAAGACTTAGAGCAATTATATGGGAAACTTGTAATTACAATTGTATTTTAGGAGGCTGAGGTAGGACTTTCACAAGTTCAGTGTCAGTCTGGGCTACATAATGAGTTTAAGCACAGCCTGAGCCACATATAGTGAAATCTTGTCTCAAAACCAAAAAAAGAATGCTTTTCATGGGGTATGCAGTTTCATCCACCACTTGTATTTTTAGCATCATCATCATCTTTTGTTTTCAAG
Seq C2 exon
GGATGGCTTACATGTAGCAGTGAAAATTGTAAAAAATGTAGGCCGTTACCGGGAGGCAGCTCGTTCTGAAATCCAAGTATTGGAGCACTTGAACAGCACTGACCCCAACAGTGTCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020385-Clk4:NM_007714:5
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=PU(6.9=95.7)
A:
NA
C2:
PF0006920=Pkinase=PU(13.2=97.5)
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:
TGAAATCGTGGACACTTTAGGT
R:
AAGACACTGTTGGGGTCAGT
Band lengths:
183-1767
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: