MmuINT0127104 @ mm9
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
PRP40 pre-mRNA processing factor 40 homolog A (yeast) [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53011992-53012562:-
Coord C1 exon
chr2:53012498-53012562
Coord A exon
chr2:53012157-53012497
Coord C2 exon
chr2:53011992-53012156
Length
341 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
ATTTTATTATTATTATTCAGTGC
3' ss Score
6.51
Exon sequences
Seq C1 exon
CGGGTGCCCTCCAATGCTTCATGGGAGCAGGCTATGAAAATGATCATAAATGATCCTCGGTACAG
Seq A exon
GTAATATGACGGTTTATAAATTTACTTTTTACGTTAATCTTAGGGTACTTAAAGTTGTATAAAATAGTATAACTCCATAAAGAGTTATTGTTCATAGCTTTGTAGTTGGCATAAATAGAGGTATTTTATGTGTGCTACAGCCAAAAACCCAAAAGACTTGTCCTACAATCTGAGCACCATGCTACACATGAAATTGGCTTTTTAGAAGCGTTTTACATCTTCAATAAATTATACAAATATTCTTAATATATGTATGAAACTTTTTTCCAAAGCCTTTACATTTGCTTCTCCAGCGTTTATTCTTATTCTTGTATGATTATTATTTTATTATTATTATTCAG
Seq C2 exon
TGCTTTAGCAAAGCTGAGTGAGAAAAAGCAGGCCTTTAATGCCTATAAAGTCCAGACGGAGAAAGAGGAAAAAGAAGAAGCAAGATCAAAATACAAAGAAGCTAAGGAATCTTTTCAGCGTTTTCTTGAAAATCATGAGAAAATGACTTCCACAACCAGATACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136-Prpf40a:NM_018785:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.455 A=NA C2=0.385
Domain overlap (PFAM):
C1:
PF0184614=FF=FE(42.0=100),PF0394210=DTW=FE(14.8=100)
A:
NA
C2:
PF0184614=FF=PD(30.0=26.8),PF0184614=FF=PU(44.0=39.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGGTGCCCTCCAATGCTT
R:
TTGTATCTGGTTGTGGAAGTCA
Band lengths:
230-571
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: