MmuINT1006650 @ mm10
Intron Retention
Gene
ENSMUSG00000009555 | Cdk9
Description
cyclin-dependent kinase 9 (CDC2-related kinase) [Source:MGI Symbol;Acc:MGI:1328368]
Coordinates
chr2:32712031-32712784:-
Coord C1 exon
chr2:32712565-32712784
Coord A exon
chr2:32712113-32712564
Coord C2 exon
chr2:32712031-32712112
Length
452 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
3' ss Seq
GTCTTTCTCTGTGCCTGCAGGGA
3' ss Score
11.11
Exon sequences
Seq C1 exon
GGAAGTGGCCGTGGAGGCGGAAGTGGCGCGGCCGCGGAGGGGCCTGGAGTGTGGCGGGACCGGGAGCGGCGGGAGCTGCGGCTGGGGGCGGCGGCGGCGGCGGCGGCGGAGGCGCGCTGGAGGTGGCCATGGCCAAGCAGTACGACTCGGTGGAATGCCCGTTCTGCGATGAGGTCACCAAGTACGAGAAACTTGCCAAGATCGGCCAAGGCACATTCGG
Seq A exon
GTAAGATTAGGCCGCGTGGGACCGCGAGCCCGGGACCTGCACTTTCCAGGGCCGACGTCGGGTCGCCCAGAGCCCGGGCCGAGGTGGTCCGGAAGCTTCTGTTTTCGTGGCTGTTGCCCGGTCTTGCTCGGCCGCGGCGCAGACGTTCCCGGCCCAACCGAGCCGACTGGCGGGGAGGAGCCTGGGGCCCGTGATGGGGGTTGGGTAGGGTTGCTGAGAGCCACTCCGAATGTGAGCGGCCACCTCTAGGGGAGGAGTAGGGGCTGAGTAGGAGTAAGCAGAGGCCGGGAGGAGGACGGAAGACACGCGGTGTGGAATGACCGCGTCCCGGATCCGAGGCCGCACCCCGCCCGCCGTGGGTCTGGGCTCCTGCTGCTCCCCTTCGCGCGGGGGAGGGGCACTCCCTGCGGAAATGCCTTATGGGTCCCTTGGGTCTTTCTCTGTGCCTGCAG
Seq C2 exon
GGAAGTCTTTAAAGCCAAGCACCGTCAGACGGGCCAGAAGGTGGCTCTGAAGAAAGTGTTGATGGAGAATGAGAAGGAGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000009555:ENSMUST00000009699:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.004 A=NA C2=0.021
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PU(27.9=38.7)
A:
NA
C2:
PF0006920=Pkinase=PU(11.1=85.7)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGGGCCTGGAGTGTGG
R:
CCCCTCCTTCTCATTCTCCATCA
Band lengths:
266-718
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