MmuINT0127101 @ mm10
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
pre-mRNA processing factor 40A [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53189969-53191225:-
Coord C1 exon
chr2:53191023-53191225
Coord A exon
chr2:53190101-53191022
Coord C2 exon
chr2:53189969-53190100
Length
922 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGG
5' ss Score
10.48
3' ss Seq
CCCTTTTTATTATTTTTCAGATG
3' ss Score
12.29
Exon sequences
Seq C1 exon
GCGGCAGTGGCCGCCGACGGAGCAGTCTGAGCCCGACGATGAGGCCGGGGACTGGAGCCGAGCGTGGAGGCCTCATGGTGAGTGAAATGGAGAGCCAACCTCCCTCGCGGGGTCCCGGGGACGGGGAGCGGAGATTGTCCGGCTCAAACCTGTGCTCCAGTTCTTGGGTCTCTGCTGACGGCTTCCTGAGGAGACGGCCCTCG
Seq A exon
GTAAGGGATCGGCGGGGTAGGGGAAAGCGGCACAATGAAAAACCGAGTCAGAGAAACAGGAAGCTCTCTCCAAACGGAGAAGAGCATATCAGGAAGAGAGCTGCAGATGGTGGGCTACGTCCCAAGGGGGAGAGATGGAGGGCGGGAACACACAAAGAAATAGGTGGGACCTTGGACTTGCCAGTGGTCTTGGCCTAGGTAGATAGATGCCTTAGGAAGAAGGAAGGTGCTGGGCCCCGGGCGGACTGTGCATCTGAGAGCCCCAGGCTTGACTTACAGTAGGGACACTTAAGTCTGTGGGACTTAAGGAGCGGCTGCTGCGGTCTTATTTCTCCGGGAGTGGTGGTGATTTGCAGGGCTTGGGGGATTCGGTTGGGAGAATTGGCTGCGGATACTTAGTTTCAAGCCAGGAACAATGGAAGTATTATATTTTAAGCTCCCTAAAACGGCATGAATTTGTTAGTGTCTGGGACAGTTTAACTCTATTAAAACATTTGTGAAGTACTCTTGGGTACCCGCACTCTGTTTTAGGTCTTGTCCATATGAATGTAATTTTAAGTAGTATAAGCTGGTTATGTGTATAAAGGTGACGGAAGTTGTGTTCATCGTAATAATTTTTTAAGTTGGAATTCAATACATAGTCACCAAGTCTGACCAGTCATTTAACAGTTTGTTAAGTCATTGGAGAGGGGTTGTAATCCGCTAATGGGTTTAACTTTTCCATTATTTTGTAAATTTTCAGGCCCCATCTAATAATCACTGTAGTGTAATTAAGATTAACTTCAGTATATGCTAATACTGTAATTTAATCACAGTGATTTAATATTGTGCCTTAATTGATGGGTTTTAGTTGTTGTTTTTGAAATGACATTTTAAAGAAGCATTTAACTGTCTCTCACTCTCCCTTTTTATTATTTTTCAG
Seq C2 exon
ATGGGGCATCCTGGCATGCATTATGCACCAATGGGCATGCACCCTATGGGTCAGAGAGCAAACATGCCTCCTGTACCTCATGGAATGATGCCACAGATGATGCCCCCTATGGGAGGGCCTCCAATGGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136:ENSMUST00000076313:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.967 A=NA C2=0.891
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACGGAGCAGTCTGAGCCC
R:
TTGTCCCATTGGAGGCCCTC
Band lengths:
320-1242
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