MmuINT0127136 @ mm9
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
PRP40 pre-mRNA processing factor 40 homolog B (yeast) [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99145009-99145411:+
Coord C1 exon
chr15:99145009-99145125
Coord A exon
chr15:99145126-99145273
Coord C2 exon
chr15:99145274-99145411
Length
148 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGG
5' ss Score
2.87
3' ss Seq
CTGTTTCCCTTTGCCTTCAGCTG
3' ss Score
10.21
Exon sequences
Seq C1 exon
GATCGGGGCTTCTGTGTGGAGGTGAACACAGCATTTGAGGACTTCGCCCACGTCATAAGCTTTGACAAGAGGGCTGCTGCGCTGGACGCAGGCAACATCAAGCTGACCTTCAATAGT
Seq A exon
GTGAGGGGACGGGCAAGCCTGGGTGGTCCTCTCACTTACCCCAATGTCTTGTTCCTCCTAACTGCCCTGCTGATTATCTTGGGTTTGGGACACATCTTCCTACCTCTTAAGGTACCCCTGACCCTATTCTGTTTCCCTTTGCCTTCAG
Seq C2 exon
CTGCTGGAAAAAGCAGAGGCACGGGAGAGGGAACGGGAAAAGGAGGAGGCCCGAAGGATGCGGCGCAGAGAAGCTGCCTTTCGAAGCATGCTGAGGCAGGCCGTGCCTGCTCTGGAGCTGGGCACTGCCTGGGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007-Prpf40b:NM_018786:19
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=0.306
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0184614=FF=PU(46.2=52.2)
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:
GATCGGGGCTTCTGTGTGGAG
R:
GCAGTGCCCAGCTCCAGAG
Band lengths:
245-393
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: