MmuINT0127143 @ mm9
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
PRP40 pre-mRNA processing factor 40 homolog B (yeast) [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99146674-99147438:+
Coord C1 exon
chr15:99146674-99146811
Coord A exon
chr15:99146812-99146891
Coord C2 exon
chr15:99146892-99147438
Length
80 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAT
5' ss Score
6.38
3' ss Seq
GTCACACCTTTGCTCAACAGACA
3' ss Score
6.72
Exon sequences
Seq C1 exon
ACCAGTCCTGACAGTGAGACGGACCCCGAAGACAAAGCTGGTAAGGAGAGTGAAGACAGAGAACAGGAACAGGACAGGGAACCCCGGCAGGCAGAGCTCCCTAACCGTTCCCCAGGCTTCGGAATCAAGAAGGAGAAG
Seq A exon
GTGAATGGGAGGACCTGGCTTTCGCCCCAGCCTGTGACACAGACTAGGGGGCTCAGGTAAGTCACACCTTTGCTCAACAG
Seq C2 exon
ACAGGCTGGGACACGTCAGAAAGCGAGCTGAGTGAGGGGGAGCTGGAGAGGCGAAGGCGGACACTCCTACAGCAGCTGGACGACCACCAATGACCCCACGAGCTACTTTCTGCCTTGGACTTCGTGAGGCAGTGGCTCCAGGGTCGCCTCAGCATCTGCCTCAGACTCCTTCGTCTTGTCTGGTCTGTGTCCACTTTTCCTAAAGTAACCCACCCCCAACACACTACTGTTAGCACCTCTCAAGGTTGCTTTTGGTGTTCAAGGGTCCCCTAGTTCTCAGACTAGTGCAGTCCTTGCCCTCAGCCCCAGACCAGAGATGGGCAGTCTATACCACGGGGTGGGTGATGCCAGTAGATAGTGTGAGAAGGGGTCTCCAGGAAAGAGACAGGCTGCTTGGACACAGCCTGGGTGGCCGAGGGCAGGGTCCTCACCCTCTAGCATCAGTGCCTGCTCTTGCCTGACCTGGCCCTGGGGCTCCACCACTACTTCCTCTCCCCTGGGACCCGATGTATGTGTTCTGTTTTGTTTTTTAAATAATATTTATAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007-Prpf40b:NM_018786:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTCCTGACAGTGAGACGGA
R:
CCTCACTCAGCTCGCTTTCTG
Band lengths:
173-253
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: