MmuINT0032850 @ mm10
Intron Retention
Gene
ENSMUSG00000026490 | Cdc42bpa
Description
CDC42 binding protein kinase alpha [Source:MGI Symbol;Acc:MGI:2441841]
Coordinates
chr1:180149153-180150258:+
Coord C1 exon
chr1:180149153-180149237
Coord A exon
chr1:180149238-180150134
Coord C2 exon
chr1:180150135-180150258
Length
897 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TATTATTTTCTTTCTCACAGAAG
3' ss Score
9.63
Exon sequences
Seq C1 exon
GTCCGACCTTTAAACACTGAAGGATCATTAAATCTCTTAGGATTGGAGACCATTAGATTAATATATTTCAAAAATAAGATGGCAG
Seq A exon
GTAAGGAAATATATTAATAGGATCATTTCAGTGGAAATATTACAACAGTCCAAGGCATTTGGATATGAAGTGCCTTCCACCCACATTTGAATCAGGCATCTCTCACTCTGGAGTATGTGATATGCACTGTCAACCTCTGGCAAGACAATAAAGACAAGCTGTAAGCAAACTATCTGTTTATGCTATGTGACTGTATAGGCAGAATGTCTGACTGACACACGTTTTCCTGAGGAGCACCCAGGTAGGAAGAAAAGTGAGAGCTGGATCTGTCGTCTATGCCTGTGGTACTGTAGACATAGTCATTCGGCCTACATTAGGAACACTTGTCCAGAGTCGCAGTGTTCCACAGCCATTCCACAGAATCTCTGAAGTACTGAAGACAATCTAGGAAGAGGCTAAGAAGGTCACAGGAGTGAGCCCCCAGAGTCAGGGCTTAGACCAGGAATCCAGGAAAGTGAGGATGGGGGAAAATAACCTGTGGGAAGGAGGACGTTTCTCGGGGCTGAGAGGCAGTTCCGCAGTTTAAAGAGCACGCTGCTCTTTGAGAGGACTGGAACCACCAGACGCACTTATTACAGGACAGAGAAGACAGTGTAAAGAGTAGGTAGAGTGACTGGTTAAAGGCATGACACCAAGACAGCTATAGTTTCCTCCAGCAAAAGTGTAGTATCTTTTACTTATAATCAAAAGTGAGACTGTTTTGTAAGCTATGCTAATTTCAGTATGTATTTTTTTGCGTATTCCATGGAAAATTATTGCTTGCTTTCTGATTTTTAGTACATAATTCTTTAACTATCACAGTTGTACACACGGTATAATTGATTACAACATCACAGAGACCAATGGATAGGAAGAACTTTAACAATCTAAACAATATTATTATTTTCTTTCTCACAG
Seq C2 exon
AAGGGGATGAACTTGTGGTTCCTGAAACATCAGATAATAGTCGGAAACAAATGGTTAGAAATATCAACAACAAACGGCGTTACTCCTTCCGAGTCCCTGAAGAAGAGAGGATGCAACAGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026490:ENSMUST00000111117:32
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=0.842
Domain overlap (PFAM):
C1:
PF0078017=CNH=PD(2.6=24.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCGACCTTTAAACACTGAAGGA
R:
CTCCTCTGTTGCATCCTCTCT
Band lengths:
209-1106
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