MmuINT0127140 @ mm9
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
PRP40 pre-mRNA processing factor 40 homolog B (yeast) [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99145914-99146331:+
Coord C1 exon
chr15:99145914-99146012
Coord A exon
chr15:99146013-99146153
Coord C2 exon
chr15:99146154-99146331
Length
141 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAG
5' ss Score
7.1
3' ss Seq
AGTATTACTCCTCTGCCTAGGGC
3' ss Score
5.5
Exon sequences
Seq C1 exon
ACTGAATGCCAGCACCTCCACACCAAAGGCCGAAAGCATGGCAGAAAGGGCAAGAAACACCATCGCAAGCGTTCACACTCACCCTCAGTGAGTCGGCAG
Seq A exon
GTAGAGGGACATGGGTGAGGCTGGACTGTTTCATACAAATTAAACACCTCTCCCCATACATTACCTCCTTGGCTCTGAACTCCCTGTCCCCAGTTCCTAGATGAGGGCTTCTGGGCTGACCAGTATTACTCCTCTGCCTAG
Seq C2 exon
GGCTCTGAGTCAGATGAAGAGGAGCTGCCCCCACCATCCCTCCGGCCCCCCAAGCGGAGGAGGCGGAACCCCTCAGAATCTGGCTCTGAGCCCTCCTCCTCACTTGATTCAGTTGAAAGTGGGGGTGCTGCTCTTGGAGGACCAGGCTCCCCATCTTCCCACCTTCTTCTTGGGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007-Prpf40b:NM_018786:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.904 A=NA C2=0.976
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF046908=YABBY=PD(31.5=46.7),PF063756=BLVR=PD(20.9=23.3)
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:
CTCCACACCAAAGGCCGAAAG
R:
AGAAGGTGGGAAGATGGGGAG
Band lengths:
251-392
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: