MmuINT0127148 @ mm9
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
PRP40 pre-mRNA processing factor 40 homolog B (yeast) [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99135972-99136502:+
Coord C1 exon
chr15:99135972-99136082
Coord A exon
chr15:99136083-99136381
Coord C2 exon
chr15:99136382-99136502
Length
299 bp
Sequences
Splice sites
5' ss Seq
GAGGTCCTG
5' ss Score
-2.13
3' ss Seq
TTTGACCCCTCCCCTTACAGCTG
3' ss Score
11.98
Exon sequences
Seq C1 exon
AGGGCCTTATGGAGTGAGCACGTAGCCCCTGACGGGCGCATCTACTACTACAATGCTGATGATAAGCAATCCGTGTGGGAGAAGCCCAGCGTACTCAAGTCTAAGGCAGAG
Seq A exon
GTCCTGAGTGGGGCTTTCTGGTTCTTCCTTTCAGCTTCCCTGGTCCTTCCAAGTTCTCGCCTCCTTTGAGCCTCCAACCATTCTCATTGTGGTTCCTCTGACCCCAAGATCCCTGACCACCTCCATGCTCCTCGTAACTGCCTCCCTAGGTTCTTAGGAAGTCCACTTCCCCCTCAGCAAGGCCAGGTGGCAACTAAAGACTATTGTCTTTCCTGTCTTGTACTCACTGGGTCCCCTTAGCCCCTGCCAGGCTGGCGAGCACTCCAGGTGCTGATGATTTTTGACCCCTCCCCTTACAG
Seq C2 exon
CTGCTGCTGTCCCAGTGTCCCTGGAAAGAGTATAAGTCAGATACAGGGAAGCCTTACTACTACAACAACCAGAGTCAGGAGTCCCGGTGGACTCGGCCCAAGGACCTGGATGACCTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007-Prpf40b:NM_018786:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.322 A=NA C2=0.653
Domain overlap (PFAM):
C1:
PF0039721=WW=PD(90.3=75.7)
A:
NA
C2:
PF0039721=WW=WD(100=73.2)
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:
AGGGCCTTATGGAGTGAGCAC
R:
CTTCCAGGTCATCCAGGTCCT
Band lengths:
232-531
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: