MmuINT0032844 @ mm10
Intron Retention
Gene
ENSMUSG00000026490 | Cdc42bpa
Description
CDC42 binding protein kinase alpha [Source:MGI Symbol;Acc:MGI:2441841]
Coordinates
chr1:180139723-180141558:+
Coord C1 exon
chr1:180139723-180139804
Coord A exon
chr1:180139805-180141341
Coord C2 exon
chr1:180141342-180141558
Length
1537 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TGACTATTAAATTGTTTTAGGTC
3' ss Score
9.69
Exon sequences
Seq C1 exon
AGATGAAGAATTTTCTGTGAGTTCAGTCTTAGCTTCTGATGTTATTCACGCAAGTCGAAAAGATATCCCCTGTATATTCAGG
Seq A exon
GTAAGTCTATGAGTCGAAAAGATATCCCCTGTATATTCAGGGTAAGTCTGTGGATGACTGAGCACATACAGGCTTTGGGTTTGTGCACATTTGTTTGTGTGCACACATGTTTGTGTGCACATGCATGTGAAGGGTAGACGGTGACATCAGCTATCTTCCTTGACTGCTCTCCACATTGTTTACTGAGATGGAGTCTCACTGAACCTGCTGCTAGCAGCTGTAGCTAGTTTAGCTCGCCAGTTTGCCCCAGCCATTCCTGGCTCTACCTCTGGAGCTCTGGGGCAACAGACAAACCCACCTAGCTCTTACCTGGGTTCTGGGGATCCAAACTCTGACCCTCAGGTTTGTGTAGCATGTGCTTTATCCACTGAGCCAACTCTCCAGCACCTAATTACTTGTTTTTAATGAATATATTTTGCTACTCTGTATAAATCATAAAGTTACTGGAACAACACCTAGACCTAGTACTCATTTATGTATCCGTACCATCCATGGATGCAAAATTGTGCTAAGACTTGTAGAATACATCAGTGTTTCTAAAGTATTCTTCATGTTCTATAATGTTTTTGAGTCCCAGTTAACCTCTAAATAAATATTATCTCATGCAGTTCTTCAAATTAAAAAAAAAAAGTTGCTCTCTATAAAACTCTCATTGTAAAAATTGTGATTCAGTTGTCTACTTCTTTATAACAAATATTCCAAAATGTGAATAGTGCTCGTCTGTCTCTGTTGTGTATGAATCTTACATCCAAGGAAGGTCAGAGATTAAACCTAGTCTCTCACTTTCCAGGCCAGCAGCTGTTTATTCTCCCCTAGCTATCTAGGGAGCCTATAAAGGTTCACTTACCTGTAACTAATTTGCAGTAGAATTGTATTGTCACTGATGTTTAAAGCATATGTAAGTATGTAAAGGGTGTCTATACATTTATGTAGCGTGTATATTATATACATAATAAATAATAGCTTAAAAGTGCTCTGATTGATTTGTAAACTTTATTTGCATACTGTTTCTAGTGCTCTTGTCTTCTTTAATGAGAATATAAAAGGTTGTCAGGAAGCACTAAGACTTTGGGAACAGTCTGATGCAGTGCTTCAGAGCACTGGGACGCGCTCTGCTCCACGCTCGTGAGATTGCTCACTTTCCCTTTACCGTGGAGTCTCACATAGACGCTTAGGTTATAATCATACTTGTTGTCTCCTGAAGCTGTTAAGGGGTGAAATGAGTTAATACTTGTAAGTTACTTTTCTTCCTGGTACTTGATAATTTTGTGTCAGTTATGAAATTGGTGTCTACATTATTTTATAGCATTATGTAACACAGCATGAAATGAAAGTCACACTTGGACTTGTATCACCTCCTGCTGTTTGAATTGTAGTGTTACAGTGAGACACTTTCACTCAGTGCAACTAAAGTGTGCTAAAGTGATAATTTAATAAATGCTCATTTTACTGATGAGTGCTAAGCAGATGAGCGTAATTCTGAAGCTAGCATTAGAGATGTCTGTTTTCTAATATTGTGACTATTAAATTGTTTTAG
Seq C2 exon
GTCACAGCTTCCCAGCTCTCAGCACCTAGTAACAAATGTTCCATCCTGATGCTAGCAGACAGCGAGAATGAGAGGAGTAAGTGGGTGGGAGTGCTGAGTGAACTCCACAAGATTCTGAAGAAAAACAAGTTCAGAGACCGCTCAGTGTATGTCCCCAAGGAGGCGTACGACAGCACGCTACCCCTCATTAAGACAACGCAGGCCGCTGCAATCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026490:ENSMUST00000111117:27
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:
NO
A:
NA
C2:
PF0078017=CNH=PU(1.9=6.8)
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:
TGAAGAATTTTCTGTGAGTTCAGTCT
R:
CTATGATTGCAGCGGCCTG
Band lengths:
296-1833
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