MmuINT0033815 @ mm10
Intron Retention
Gene
ENSMUSG00000009555 | Cdk9
Description
cyclin-dependent kinase 9 (CDC2-related kinase) [Source:MGI Symbol;Acc:MGI:1328368]
Coordinates
chr2:32709467-32709944:-
Coord C1 exon
chr2:32709773-32709944
Coord A exon
chr2:32709616-32709772
Coord C2 exon
chr2:32709467-32709615
Length
157 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGG
5' ss Score
8.99
3' ss Seq
CGGTACCCTCTTCTTCTCAGGAG
3' ss Score
6.77
Exon sequences
Seq C1 exon
ATCCTGCACAGGGACATGAAGGCTGCGAATGTGCTCATTACCCGGGATGGGGTCCTGAAGCTGGCAGATTTTGGGCTGGCCCGTGCCTTCAGCCTAGCTAAGAATAGCCAGCCCAACCGATACACCAACCGTGTGGTGACATTGTGGTACCGGCCTCCGGAGCTGCTGCTCG
Seq A exon
GTGAGGACTCCCGAGCGGGCAGAGGGGGGCAGGGGCCGGGTGCCTACCTGGCCACAGCCCCCATTGCCTGGGGCCTTTTGAGCCATCAGCTCTGGGACGTGGAGTCTCAGGAGGCCCTTGGGCTTAAGAGGCACTCCCGGTACCCTCTTCTTCTCAG
Seq C2 exon
GAGAGCGGGACTACGGCCCGCCCATTGACCTTTGGGGTGCTGGGTGCATCATGGCAGAGATGTGGACTCGTAGCCCTATCATGCAGGGTAACACAGAGCAGCACCAGCTCGCCCTCATCAGCCAGCTCTGTGGCTCCATCACCCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000009555:ENSMUST00000009699:5
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(19.2=100)
A:
NA
C2:
PF0006920=Pkinase=FE(16.5=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:
AAGGCTGCGAATGTGCTCATT
R:
GTGCTGCTCTGTGTTACCCTG
Band lengths:
258-415
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