MmuINT0127110 @ mm10
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
pre-mRNA processing factor 40A [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53145620-53145915:-
Coord C1 exon
chr2:53145824-53145915
Coord A exon
chr2:53145737-53145823
Coord C2 exon
chr2:53145620-53145736
Length
87 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
ACAAGATTTCTGGCTTTTAGGAT
3' ss Score
7.24
Exon sequences
Seq C1 exon
GATCAACTGCACTTGATCTTTTCAAGTTTTATGTTGAAGATCTTAAAGCACGATATCATGATGAAAAGAAGATAATAAAAGACATTCTGAAG
Seq A exon
GTAAGTGAACTTGTTCTTAACTATTTGAAAACATTGATTCATTCCTTGCAGTTACATGTTATTTATAACAAGATTTCTGGCTTTTAG
Seq C2 exon
GATAAAGGATTTGTAGTTGAAGTAAACACTACTTTTGAAGATTTTGTGGCAATAATCAGTTCAACCAAAAGATCAACTACTTTGGATGCTGGAAATATCAAGTTGGCTTTCAATAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136:ENSMUST00000076313:18
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=0.000
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(17.9=32.3)
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:
TCAACTGCACTTGATCTTTTCAA
R:
TCCAGCATCCAAAGTAGTTGATCT
Band lengths:
183-270
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