MmuINT0127138 @ mm10
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
pre-mRNA processing factor 40B [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99314843-99315286:+
Coord C1 exon
chr15:99314843-99314980
Coord A exon
chr15:99314981-99315190
Coord C2 exon
chr15:99315191-99315286
Length
210 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGA
5' ss Score
5.24
3' ss Seq
CAGTGCTCTCCCCGTTCAAGGTC
3' ss Score
6.9
Exon sequences
Seq C1 exon
CTGCTGGAAAAAGCAGAGGCACGGGAGAGGGAACGGGAAAAGGAGGAGGCCCGAAGGATGCGGCGCAGAGAAGCTGCCTTTCGAAGCATGCTGAGGCAGGCCGTGCCTGCTCTGGAGCTGGGCACTGCCTGGGAAGAG
Seq A exon
GTCAGAAGCACAGCCTGGCCCCAATCACCCTCAGGCCTGAGGGCAGCGGAGCTTCTCCACCACTGAGGGCCCACCCCAGTCACAGCACAAGCCCTGGGCCAGCTCCAGTTCCCTTCCTTCCTCTGCCCCAGCCCTGCCCAGTTCTCGTGGCGGTGTCCAAGCTGGTCCAGGCAGGGCCTGGTCTGATCAGCAGTGCTCTCCCCGTTCAAG
Seq C2 exon
GTCCGTGAGCGCTTTGTGTGCGACTCAGCCTTTGAGCAGATCACCCTGGAGTCGGAGCGGATCCGGCTCTTCCGAGAGTTCCTGCAGGTGTTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007:ENSMUST00000145482:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.301 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0184614=FF=PU(46.2=52.2)
A:
NA
C2:
PF0184614=FF=PD(50.0=81.2)
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:
GAAAAAGCAGAGGCACGGGAG
R:
CTCCAACACCTGCAGGAACTC
Band lengths:
228-438
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