MmuINT1027483 @ mm10
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
pre-mRNA processing factor 40A [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53152958-53153528:-
Coord C1 exon
chr2:53153464-53153528
Coord A exon
chr2:53153123-53153463
Coord C2 exon
chr2:53152958-53153122
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:ENSMUST00000076313:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.227 A=NA C2=0.348
Domain overlap (PFAM):
C1:
PF0184614=FF=FE(42.0=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
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
- 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