MmuINT0127131 @ mm10
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
pre-mRNA processing factor 40B [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99307822-99308341:+
Coord C1 exon
chr15:99307822-99307930
Coord A exon
chr15:99307931-99308190
Coord C2 exon
chr15:99308191-99308341
Length
260 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
TTAACCCTGTGTCTTCCCAGGAA
3' ss Score
10.29
Exon sequences
Seq C1 exon
GCGGGCAGAACAGACTTTTGGGGACCTGGAGGTCTGGGCTGTGGTCCCTGAGAGAGAGAGAAAGGAAGTTTATGATGATGTCCTCTTCTTCCTGGCCAAGAAGGAGAAG
Seq A exon
GTAATGGACACTCACGGGCTGGACTCTGCTGCTCTCCATTTCTTGTGGACCTGGTTGCTCAGTGTCCCTTCTCCTGAATTGGAAGCTGGTGTGGAACTTTGTCCCGAGCCAATAACCCTGGGTGAGGGAGGGCAAGGACGACACTGGTTTGTGACCTGGGATTCCTCTCCTTTGTGGGACCCAGAAGTCTTGAGTCTTGTCCTCCTTTCCAGGATCCTCCCATGCTGGCCCTGCCTCACTTTAACCCTGTGTCTTCCCAG
Seq C2 exon
GAACAAGCCAAGCAGCTCCGGCGTCGGAATATCCAGGCCCTGAAGAGCATCCTGGATGGGATGAGCAGTGTCAACTTCCAAACCACTTGGTCCCAGGCCCAGCAGTACCTCATGGATAACCCCAGCTTTGCTCAGGACCAGCAGCTGCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007:ENSMUST00000145482:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF0394210=DTW=PD(4.3=13.5)
A:
NA
C2:
PF0184614=FF=PU(75.0=82.4)
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:
GCGGGCAGAACAGACTTTTGG
R:
TCTGCAGCTGCTGGTCCT
Band lengths:
260-520
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