MmuINT0127139 @ mm9
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
PRP40 pre-mRNA processing factor 40 homolog B (yeast) [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99145622-99146012:+
Coord C1 exon
chr15:99145622-99145717
Coord A exon
chr15:99145718-99145913
Coord C2 exon
chr15:99145914-99146012
Length
196 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
TCTCCCTCTGCCTCTAGCAGACT
3' ss Score
7.01
Exon sequences
Seq C1 exon
GTCCGTGAGCGCTTTGTGTGCGACTCAGCCTTTGAGCAGATCACCCTGGAGTCGGAGCGGATCCGGCTCTTCCGAGAGTTCCTGCAGGTGTTGGAG
Seq A exon
GTAAGGCACTTGGCCACCCTGATCTATGTATCTTTGAACTCTAGGCTTGCATGAGACCTTCAATAGCTTGTCACCGTAAAGGCTCTTTTACCTGCCCAGCTAAAGAAGGGAAGGACTGAGGGTGCCCTAGAATAGACAGAGGGCCCTAGCTGAGACAGGAAGGCAAGGTTCTCACCTCTCCCTCTGCCTCTAGCAG
Seq C2 exon
ACTGAATGCCAGCACCTCCACACCAAAGGCCGAAAGCATGGCAGAAAGGGCAAGAAACACCATCGCAAGCGTTCACACTCACCCTCAGTGAGTCGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007-Prpf40b:NM_018786:21
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=0.904
Domain overlap (PFAM):
C1:
PF046908=YABBY=PU(29.2=78.8),PF063756=BLVR=PU(26.9=54.5)
A:
NA
C2:
NO
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:
TCCGTGAGCGCTTTGTGTG
R:
CTGCCGACTCACTGAGGGT
Band lengths:
194-390
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: