MmuINT0127144 @ mm9
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
PRP40 pre-mRNA processing factor 40 homolog B (yeast) [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99134472-99134921:+
Coord C1 exon
chr15:99134472-99134615
Coord A exon
chr15:99134616-99134855
Coord C2 exon
chr15:99134856-99134921
Length
240 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
GCTGGTCTTTATATCCATAGATA
3' ss Score
7.44
Exon sequences
Seq C1 exon
ATGCCCCCTCCAGGGCTCCCACCTCCTTTTCCTCCGATGGGGCTCCCCCCTATGAGTCAGAGACCACCAGCCATTCCCCCCATGCCACCTGGCATACTGCCCCCAATGCTTCCACCAATGGGGGCACCGCCACCACTTACACAG
Seq A exon
GTAACTCTGCTTTCCACAGGGGTCTTTAGCTGGAAGGGAGCTGGGAGGGAAGGGAATGTTGGGCTAGATGCATGCCTATTTGTCTGCTGAGTGACTAAAGCAGTTTTTAGGCATGTGACTGCCCAGAACCTGAAGACTATCAGAGTGTGTACCCATGGTGAGGGTCGGAACCCCAAAGGGATCTTCTTTTGCCTCACTCTTCCTCACCCTAACATTGGCTGCTGGTCTTTATATCCATAG
Seq C2 exon
ATACCAGGAATGGTCCCTCCAATGATGCCGGGGATGCTGATGCCAGCGGTGCCTGTCACTGCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007-Prpf40b:NM_018786:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.970 A=NA C2=0.416
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGGCTCCCACCTCCTTTTC
R:
AGGCACCGCTGGCATCAG
Band lengths:
188-428
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: