MmuINT0127134 @ mm10
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
pre-mRNA processing factor 40B [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99309685-99310035:+
Coord C1 exon
chr15:99309685-99309799
Coord A exon
chr15:99309800-99309943
Coord C2 exon
chr15:99309944-99310035
Length
144 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
CCATCTCTCCCTTTCTGCAGGCT
3' ss Score
10.99
Exon sequences
Seq C1 exon
AGCTTCCTGGACGAGCTGCATGAGACAGGGCAGCTGCACTCCATGTCCACCTGGATGGAGCTGTACCCGGCAGTCAGCACTGACGTTCGCTTTGCCAACATGCTGGGCCAGCCGG
Seq A exon
GTAAGGCAGCCAGGCTTCCCCTTGTCTGCTCTGCTTTCCTACCCTGTCAGCCTCTCTGGACCTAACTCCCTGGTCCTGGCCGTGACCCTACCCTGAGCCTTGGGAAGCTGCCGCCCGCCAGGCCCCATCTCTCCCTTTCTGCAG
Seq C2 exon
GCTCTACTCCTTTGGACTTGTTCAAGTTCTATGTGGAGGAGTTGAAGGCTCGATTCCACGATGAGAAGAAGATCATAAAGGATATCCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007:ENSMUST00000145482:17
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:
PF091066=SelB-wing_2=PD(48.8=51.3),PF0184614=FF=FE(67.9=100)
A:
NA
C2:
PF0184614=FF=PD(17.9=32.3)
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:
CTTCCTGGACGAGCTGCATG
R:
CCTTTATGATCTTCTTCTCATCGTGG
Band lengths:
194-338
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