MmuINT0127149 @ mm9
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
PRP40 pre-mRNA processing factor 40 homolog B (yeast) [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99136382-99136617:+
Coord C1 exon
chr15:99136382-99136502
Coord A exon
chr15:99136503-99136592
Coord C2 exon
chr15:99136593-99136617
Length
90 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GCTCTCTTTTCCCCTTGCAGCCC
3' ss Score
11.95
Exon sequences
Seq C1 exon
CTGCTGCTGTCCCAGTGTCCCTGGAAAGAGTATAAGTCAGATACAGGGAAGCCTTACTACTACAACAACCAGAGTCAGGAGTCCCGGTGGACTCGGCCCAAGGACCTGGATGACCTGGAAG
Seq A exon
GTGAGGCATGCTGGAGGTAGAGGGGGAAGACTGGGCAAGGCTGCTGGGAGTCCTTTGCTATCCCGTGACTGCTCTCTTTTCCCCTTGCAG
Seq C2 exon
CCCTCGTCAAACAAGAGTCTGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007-Prpf40b:NM_018786:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.653 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0039721=WW=WD(100=73.2)
A:
NA
C2:
NO
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:
CTGCTGTCCCAGTGTCCCT
R:
CCTGCAGACTCTTGTTTGACGA
Band lengths:
143-233
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: