MmuINT0127103 @ mm9
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
PRP40 pre-mRNA processing factor 40 homolog A (yeast) [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53012498-53013106:-
Coord C1 exon
chr2:53012998-53013106
Coord A exon
chr2:53012563-53012997
Coord C2 exon
chr2:53012498-53012562
Length
435 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTC
5' ss Score
6.8
3' ss Seq
TTCCTTTAAATCATTTTCAGCGG
3' ss Score
7.83
Exon sequences
Seq C1 exon
TTTTACTCCTAAAAAAGAAGAGGAAGAGAGCCAACCAGCAAAAAAAACATATACTTGGAATACAAAGGAGGAGGCAAAGCAAGCATTTAAAGAATTATTGAAAGAAAAG
Seq A exon
GTATTCTAGATTTTTTTAAGTATCGTAATAATTTCCTAATAAATGTTCACTTTGATGCCTTTATTTAAAATACTAATCTCTAGAACTGTTGTAACTGACAGCAAACTAAATTTGTTGTGTTTTAATTGAACGCTTTTGTGAAACTTAAAAAGGTATTAATTTCACAAGCATATTTTTGCCTTGATGTTTAAGATTTTTTTCAAAAAACTTAAATCATCCTTTTATTGATGGACTAATACAGAAAAATACTGTTTCAATTTCAGTGTGAATTTGTTTTCACAAAATTGCTTCATTAAAAATGGCTTTAGACTTTAAAAAAATCTACAAAAGGAGGTGCTTGGTATTTGCAGTGAGCATTATACTTGCCTTCCCATGACACTGTTACTCTCTGTGTTCTTGTATTCAATACTCATTTTTCCTTTAAATCATTTTCAG
Seq C2 exon
CGGGTGCCCTCCAATGCTTCATGGGAGCAGGCTATGAAAATGATCATAAATGATCCTCGGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136-Prpf40a:NM_018785:11
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.811 A=NA C2=0.455
Domain overlap (PFAM):
C1:
PF0184614=FF=PU(24.0=32.4),PF0394210=DTW=FE(25.4=100)
A:
NA
C2:
PF0184614=FF=FE(42.0=100),PF0394210=DTW=FE(14.8=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: