MmuINT0127123 @ mm10
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
pre-mRNA processing factor 40A [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53159263-53159678:-
Coord C1 exon
chr2:53159558-53159678
Coord A exon
chr2:53159317-53159557
Coord C2 exon
chr2:53159263-53159316
Length
241 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTTGATTCCATTGAAACTAGGAT
3' ss Score
4.7
Exon sequences
Seq C1 exon
CAACTATTGTCTAAATGCCCATGGAAAGAGTACAAATCTGATTCCGGGAAGCCTTATTACTATAATTCTCAAACAAAGGAGTCCCGCTGGGCCAAACCTAAGGAACTTGAAGATCTTGAAG
Seq A exon
GTAAGATGGGAAAACAATTCTACTGGGAAGTTGTTGTGCATATATCAGTCACCTGGAAACAGTCCTCCCTGAATAGGATTATTCAAACTAAGGCCTTATTCTTTTTTAAAAAATAATTAAAGTTTATGCAAATTTTAAATGATGTAACATTTTTTGTGGGCTCTTATTTTCTTGTTGCTCTAGATCTCAGTTCTATAGATTTTAAATAGATTTTTATTTGATTTGATTCCATTGAAACTAG
Seq C2 exon
GATACCAGAATACCATTGTTGCTGGAGGTCTTATTACAAAATCAAACCTGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136:ENSMUST00000076313:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.449 A=NA C2=0.085
Domain overlap (PFAM):
C1:
PF0039721=WW=WD(100=73.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAACTATTGTCTAAATGCCCATGGA
R:
TGCAGGTTTGATTTTGTAATAAGACC
Band lengths:
173-414
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