MmuINT0127141 @ mm10
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
pre-mRNA processing factor 40B [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99315723-99316148:+
Coord C1 exon
chr15:99315723-99315900
Coord A exon
chr15:99315901-99316086
Coord C2 exon
chr15:99316087-99316148
Length
186 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TTTTTTTTTAAACCCTATAGATC
3' ss Score
7.86
Exon sequences
Seq C1 exon
GGCTCTGAGTCAGATGAAGAGGAGCTGCCCCCACCATCCCTCCGGCCCCCCAAGCGGAGGAGGCGGAACCCCTCAGAATCTGGCTCTGAGCCCTCCTCCTCACTTGATTCAGTTGAAAGTGGGGGTGCTGCTCTTGGAGGACCAGGCTCCCCATCTTCCCACCTTCTTCTTGGGTCAG
Seq A exon
GTAAGCAGTTTCTAGGAGCCCGGGAACTAGAGTGCTGGGATAGAGGCACAGCAAATCCCAGACCGCTGAGGGCTGACTGGGATGGGAGGGCCTCACTGTGGAGCAAGACTTCCTATCTCTGCCCAGGCAAGGAGCTGCCTTCTCCCGATGGGACTCAGCGTAGATTTTTTTTTTTAAACCCTATAG
Seq C2 exon
ATCATGGTCTTCGGAAAACCAAGAAACCAAAAAAGAAAACCAAGAAAAGAAGACACAAGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007:ENSMUST00000145482:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.980 A=NA C2=0.982
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
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGTCAGATGAAGAGGAGCTGC
R:
CGACTTGTGTCTTCTTTTCTTGGT
Band lengths:
234-420
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types