MmuINT0127128 @ mm9
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
PRP40 pre-mRNA processing factor 40 homolog B (yeast) [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99137236-99137508:+
Coord C1 exon
chr15:99137236-99137362
Coord A exon
chr15:99137363-99137443
Coord C2 exon
chr15:99137444-99137508
Length
81 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCTG
5' ss Score
4.05
3' ss Seq
CCTGTGCCTCTCTGCTCCAGGCT
3' ss Score
10.01
Exon sequences
Seq C1 exon
CTCTACTGGACAGCATCGGCAGCCACAGGAAGAGGAGGAAGCTAAGCCAGAACCAGAGCGATCTGGCCTCAGTTGGAGCAACCGGGAGAAGGCAAAACAGGCTTTCAAAGAACTGCTAAGGGACAAG
Seq A exon
GTGCTGGGGATGGTGCTCCCAGGGAAGGCCTGGAGGGTTTGAAAGATAACAGGCTCTGAGACCTGTGCCTCTCTGCTCCAG
Seq C2 exon
GCTGTCCCTTCCAATGCTTCATGGGAACAGGCCATGAAGATGGTAGTCACTGACCCCCGCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007-Prpf40b:NM_018786:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.818
Domain overlap (PFAM):
C1:
PF0184614=FF=PU(24.0=27.9),PF0394210=DTW=PU(33.0=86.0)
A:
NA
C2:
PF0184614=FF=FE(42.0=100),PF0394210=DTW=FE(18.8=100)
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:
TCTACTGGACAGCATCGGCAG
R:
CCATCTTCATGGCCTGTTCCC
Band lengths:
169-250
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: