MmuINT0127115 @ mm10
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
pre-mRNA processing factor 40A [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53141767-53142029:-
Coord C1 exon
chr2:53141943-53142029
Coord A exon
chr2:53141864-53141942
Coord C2 exon
chr2:53141767-53141863
Length
79 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGA
5' ss Score
10.53
3' ss Seq
TCTGTATGTGTATTGTTTAGGGA
3' ss Score
7.94
Exon sequences
Seq C1 exon
CATGAATGTCAGCATCATCATTCAAAGAACAAGAAACATTCTAAGAAATCTAAAAAGCACCATAGGAAACGCTCCCGCTCTCGATCG
Seq A exon
GTAAGAAGTGTGTTGGCTGGCACAGTAGACCAAAACATTTGTGAACATGCTTGTGAATGTCTGTATGTGTATTGTTTAG
Seq C2 exon
GGATCAGAGTCAGATGATGACGACAGCCATTCAAAGAAAAAAAGGCAGCGATCAGAGTCTCATTCTGCTTCAGAGCGTTCGTCCAGTGCTGAGTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136:ENSMUST00000076313:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTCAGCATCATCATTCAAAGAACA
R:
CAGACTCAGCACTGGACGAAC
Band lengths:
178-257
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