MmuINT0037438 @ mm9
Intron Retention
Gene
ENSMUSG00000020385 | Clk4
Description
CDC like kinase 4 [Source:MGI Symbol;Acc:MGI:1098551]
Coordinates
chr11:51080673-51085524:+
Coord C1 exon
chr11:51080673-51080833
Coord A exon
chr11:51080834-51085301
Coord C2 exon
chr11:51085302-51085524
Length
4468 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAAT
5' ss Score
4.94
3' ss Seq
ATCCTTTAATGTGTTCGCAGTCA
3' ss Score
6.32
Exon sequences
Seq C1 exon
ATGCGGCATTCCAAACGAACTCACTGTCCTGATTGGGATAGTAGAGAAAGCTGGGGCCATGAAAGCTACAGTGGAAGTCACAAACGCAAGAGAAGGTCTCACAGCAGTACTCAGGAGAACAGGCACTGTAAACCACATCATCAGTTTAAAGACTCGGATTG
Seq A exon
GTAAATGACTTGCATTTTAAGTTTCAGCAAGTTGTCATTTGCTTATATAGCTTTTATCAAATTTGGAATCAGACATATTTACTCCTGCAAAAAATAAAAAAGTTAACAATATCATAGGCTAGTTTCTATACTGCCTAGACTAAAGCTATGAATTTTATAGTTTGTTCTATGTCTGTCTGGGATTGATAGGAGACAGTAGCTCAGCAAGTGACTAAACTAAGGGCTCTGAGGATTTAGCTCAGTGTTAGAACACTTGTTACCCAATATATGTGAGGTCCCAAAAATCCTTAGAAACCCTTCCATCAAAAAGGGGGAAGGAAGTCAAAAGATTATATTCAAGAACATATACAAAGTTGAATAATAATGATACTCATAGGAAGATGGCATATATATTTGGGTGTGCAAGAAGTGTTTCCCAATTGAGATGTCATAGAAAGTGGTTAATCCCGATAAGAAAAGCTACCTGAAATGCTATCTGAGACCATTAAAGTGCTTTGAGGAATAGCCATTCATGTTACATCTTACAGATTATATTAATAGAACACCAATGGATATGTCTGAGAGTTTTAGAAACTTGCTTTATATTTTGAGAATTGTTTCTACAGGCATTCTCTGGTAATTTAGGATAGAGCCTCAGTAAAAATTTGTGATAGTATGTCTTACTATAATTATGATATAAAATTTGGAGGTAATATGTTTATATAGAATTGAAAGAATCTTAAAGTTCTAAATATAAAGAAAGGCTAGGTGAGTAGTTTCTTTCACTCTGCCTTCCATTAATTTCCCTTTCTCATTTGTTTTGTTGGTTCTATGTTTTCTCCTTGTTTGTACAGATGTTCCATTGGGGCTGTTTACCAGATTGCTTTCTAAATTAGCCAGCTGGGGTTACTTTAAAAAACAGTATGTAATTTTTTTTCCTTCTCCATGCTAAACAGAGTTGTCTGCCAAAGAGCTTGTTTGTAGTTCTTGTAAACTAATCATGTTTTATCAAAGTTATGTAAGGGGTGCTGGATAAGGTTATGGCAAGATTCAGTAACCAGACTTTATTAATGAACACTGTACAAATTGTACCCCATTATTAATGAGTATAGGATACTCTTTAAGGCTTACCTTCTTATACATAGTGCTAGAGTATATATTATATATGTGAAAAAGTTGACTTGAGTGATTTTGTATTCATAATAATTATAAAAACCAGTCAGTCCAATTAATCACTAAGCCAGTACTACCATCTTTAACATTGACATCAAACAAATTTGGTGATTATTATTCATCATAATCCAGACTATTTGTTAATTGTAAATATCTTTTTGAAAGCTAAAAGTTTTATGAATATTTTAATAAATGGCTGGGCAGTTGAGGCAGCAGCAGTGTAAAGGAACAGCAGTGTGGAAAGCGTTGCGTGGCTTGACTGAATTATTTCTGTCTGTTCCTAAGGGGTCTTTGTGTACAAATCTTTGCCTGTGGCTATTTCCTGAGAGTAGATTCTAAGAAGAGGCATTTTCAAGTTAAAGGGTATGAAGTTTTACAAGGTTCTTGCTGCATATTCTCATTTCTTGTTCTAGAAAGCTTATAACATGCTCCTTGGTGCTGTCTCTAGTTTTGTCTGTTTTAAATGGTTTTCCTAACCTGAATTTCTAGTGAATTTGTTCAGATTTTCTGAAGAATTTTTATGTCAATTGTTTTCTACTAAAGTATATTTCTTTCTGATTTACAAGATGTTTTTATTATGTATTATTTTAACCCTTTGTCATATGTATTATAAAACATTTTCTCCTGATTTGTCTTTTGGCAGTAGCCTTTGATTTGGTCTCCCTTTCAGCAGGTTTAATCTATTCTGCCTCAAATACCAGGAAGACCAATGTAGATGTAATATATATATATATGCCAAATCCTTAAATATCTCCCTGTAACACAGTACCAAGTTTTAAACCTTTGGTAAACTTTATATGATTAGAAACCACCTAGGAGGTATGCAGACTTAGATTTAGAATTCAGTATGACCTGGGTCTTCATTTGTAAACTCTATAGTCAGTATTAGTGCAAATAGTCTGTCCTTTAAAAACACCTTTAGTTTGGTTGCACAGGGCTTCTAGTGACATTTGATGCATCTACTTCCTGTCTGCAGAGTAGATACATGCATTTGAAGCCTCTGGCTGGCGGTGCTGTCTGTATAAGTGTAACATGGCACTATGCTGCTCTGGAATTTCTTCTGCTTTCCACTTTGTCCAAATCCTGGCTTTCCTTTAAGATGCTTATCTGCTTCCATCTTTGTCATGACTTCTTCCTTAGTAATCTTAAGCAAATTGAATTCTTTGCCTTCCCGGAGTTCATTTGCACCTTTTCAACATTTTTCGCATTTGTCTCTTTTGATTTTCTTTTTTTTTTCTTTTTTTTTTCTTTTCTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAATCTTAAATTGTCTTACATGATTTTATTTTGTCTTCCACAGGACGGAAATAAAAAAAGCCAATTCACTTAACAGTTACTGGGCATTTAGTGGATATTTTTAAAAAGTCAAATCTGTTTATTCTGTCTACCATGTCCACAGCTTGTATAATTCTGTAGTCTTTAATCTCTAAACTTTAGTCTTTGGTTGTCATGATTGGAAAGGTCCTTCTCATGCTAGCTCTGCTCACAATAGTATCACCACCCCACTTTTTTATTGTTGGTAGATTGTTTTGGATTGTCAGCAGGGCCAGTTTCATGTCATATTCCAGTTAAAGATTATTATTAGTCTAGTTTATTTTTATGATAGACTTTGGATTTGGTGGGTGTGGGATACCTTATAAAATTAAATAGGATGCCTGTAGAATTATGACTAGCTTCTTGTTTTTCATCTAGATCTCTGCTTCAGACCAACTGTCTCAGGCCTAGAGTTTAATCCTAATAGCCTCACTTGTTTCTCCAGAAGTTAAGGAGAACTTGAGAATGATGCTAGGCAATAAGAAGGCCCAGCCTAAAATAGATGCCAGTCTTGTTGGGTTGTAGTCCTAGGGATGTTTCTATTTCTGCTTAAACAAGAACCTGGGAAAGAAAATGACAGCATATTCTGGGGAGTGTAAAGGGGTTGGCGGGGGCAGCTGCAGCAACATCTGTCACTCCATTGCTTGTCAGGATTATTTAGCTGATTTGTCTGACTGGGCAGGTGTCCCCTCTCTCCCCCAGTGCTCCATGTGCATCCCTCTTGAAGCTTCGCACTCTGTTGAAGAGGACACTCATCCCAGGTAGAGGGGGGATGGGAAACTGGGCCGATTGAATCCGTCCTTTTCTTTCCATCAGATCAGGACACTCACCTGGGATCCATTGACTTCCTGAGGTCCATGACCGTCATGAAGTTCTTGCCAAGTTTTGTTTATGTATTTGTATGTTTCTTGGGGAAAAAGGGCTCTACAACTTCCATCAGGTTCTCAAAGGAGTCTGTAGATGCACTGGGGCACTAGAAAATGCTGTTTGCTGTTTCTTGGGTATTTTTTAAGCAAGAGTCACAGGAAATTAGGCAGGTAGAATGGGAGGGATGTCCACAGTCCTGGATCCTTTCTTGTGTGGAAGGTCTGTTCACATGTGTTTGGCACACTAGGCAAGCCTCAGAAGTTCTGGTCTCTGTTTCTTAAACAAGAATAACACAAAGCTTAGACATAGAAAAGAGGAGATAGAATAGGTGACATAGGGCAGTAGTAGCAGTTTGAAAATATCTTAGTTTTTGCCACTAATAAGCTCTGCAACGATGCTGTATCATTTAGGGATCTTAATTGAATTTTAGTAAATGAAAGGGCTGAAGGACATTTAAAGCTTCTCATATCTGTGATACACATTCTATAAGAAGTCGTGGTCAGGGATATTTAAAATGCTCTTAATTTAAGGGAAAGGAATCTTCTTTTGCCCTTCTCTAAATGTGTGGCTCTGAGAGAGGAAAAGGAAGCTAGTTTCAGATGCCTATGTTGTATGATCGATCAGTGCATTTCAGAATAGGTTTGCAAGTTTGGTCTTGACTTTTTAGATGGTAAAGGAACATTCAGTCATAAGCATATTGTAATTGAAGCTTTGTTCCTTGGTATGAAATGGTTGACAGCAATTTTCTAATGTGTAGGTGTTTTTTTGTTTTTTTGTTTTGAGATGGTTTCATGTGACCCAGGCTGGCTCCAAACTTGTAGTGTACTTCAGGATGGCCTTGAATTCTTGATCCTCCTGCCCTTACCTTCCAAGTGCTGGGATTAAAGGCATGCCTGGCTGTAGCAATTTAATATGGACCTATTTGGTTAAAAATTATTTCTTAAGCTTTCCTAGATACAAATAAATTTCATCTCATTGATTTGAATTTTTTCCTTTTATTGAGATAGCTATTTAAACCAAGAATTCTTGAAAGTTTTGTTTGAACCACATTATTCCAGAATGAAGAGAATAATTTGAAATCCTTTAATGTGTTCGCAG
Seq C2 exon
TCACTATTTAGAAGCAAGATGCTTGAATGAGAGAGATTATCGGGACCGGAGATACATTGATGAATACAGAAATGACTACTGCGAAGGATATGTTCCAAGACATTACCATAGAGACGTTGAAAGCACTTACCGGATCCATTGCAGTAAATCCTCAGTCAGGAGCAGGAGAAGCAGCCCTAAGAGAAAGCGTAATAGACCCTGTGCAAGTCATCAGTCGCATTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020385-Clk4:NM_007714:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.119 A=NA C2=0.312
Domain overlap (PFAM):
C1:
PF078926=DUF1667=PU(64.0=91.4),PF053316=DUF742=PU(44.6=94.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: