MmuINT0127111 @ mm10
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
pre-mRNA processing factor 40A [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53145233-53145736:-
Coord C1 exon
chr2:53145620-53145736
Coord A exon
chr2:53145371-53145619
Coord C2 exon
chr2:53145233-53145370
Length
249 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
TAGATTTGATTTTTTGATAGTTA
3' ss Score
2.61
Exon sequences
Seq C1 exon
GATAAAGGATTTGTAGTTGAAGTAAACACTACTTTTGAAGATTTTGTGGCAATAATCAGTTCAACCAAAAGATCAACTACTTTGGATGCTGGAAATATCAAGTTGGCTTTCAATAGT
Seq A exon
GTAAGTTAAATTATTTCAGATACCTACCTAATTGTTCATCTAAGAATTACTTCAAGTTGTAGGCTAGTGGGATAAGGTACTGTAAAAGGGATAAGGTATAAGGTAAAGAAAGTAAAACAAACTGTGTAAAAATGTTTCATTGTTAGAGGTTAAATTAAACTTTTATAAGTGATGTTATAATACTTTTAAGAACAATGTCTTGTTTGAAACAGGACTCATCATAATTTAATAGATTTGATTTTTTGATAG
Seq C2 exon
TTACTAGAAAAGGCAGAAGCCCGTGAACGTGAGAGAGAAAAAGAAGAGGCTCGGAAAATGAAACGGAAAGAGTCTGCCTTTAAGAGTATGTTGAAACAGGCTACCCCTCCAATAGAACTGGATGCTGTCTGGGAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136:ENSMUST00000076313:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.543
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0184614=FF=PU(46.2=52.2)
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:
AAGGATTTGTAGTTGAAGTAAACACT
R:
TCCCAGACAGCATCCAGTTCT
Band lengths:
247-496
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