MmuINT0127134 @ mm9
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
PRP40 pre-mRNA processing factor 40 homolog B (yeast) [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99140116-99140466:+
Coord C1 exon
chr15:99140116-99140230
Coord A exon
chr15:99140231-99140374
Coord C2 exon
chr15:99140375-99140466
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-Prpf40b:NM_018786:17
Average complexity
IR-S
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
Other Skipping Isoforms:
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: