MmuINT0127118 @ mm9
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
PRP40 pre-mRNA processing factor 40 homolog A (yeast) [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:52997509-52999626:-
Coord C1 exon
chr2:52999495-52999626
Coord A exon
chr2:52998305-52999494
Coord C2 exon
chr2:52997509-52998304
Length
1190 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
TGTGTTGAATGTCTTTGCAGGGT
3' ss Score
8.68
Exon sequences
Seq C1 exon
GACTCTCCAGAATCAGATACTGAACGAGAAAAGGATAAAAAAGAAAAAGATCGGGACAGTGAAAAAGACAGAAGTAGACAGAGATCAGAATCAAAACACAAATCACCTAAGAAAAAGACTGGAAAGGATTCT
Seq A exon
GTAAGTACTGAAAAGTGTTTCTTTCCTGAATTCCCAAAAAACAACAGTTCATTCCCTCATTAAATCTTTGATGGTGTTTATAGGATTTTTTTTTCTTGATCTGCTAACATTGAAGAAAAGAATAAATTCTCTTCACTGCTTATCACAAAATAGCTTTCTGGTACCATTCATTTCCTTACCTGATTTAGGAGGAAATGCTTCTTGGGATGAAATAAAAAGAAATGTCTGAGCCGGGCGTGGTGGCTCACGTCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGCTCCAGGACAGTCAGAGCTATAAAGAGAAACTGTCTCGAAAAACCAAAAAAAAAAAAAAAGAAAGAAATGTCTGGTACCACTTCATAAATGACTATCCGGTTGATTCTCTTACATTTATATTCCTTAAAAAATTTTAACAGCAAATTAACAGTACAAAATAGTTGTCATTTAACTTGGAATGAAAAGATAATGTTTGAATTTTACAGTACCACTGAGAAGTACATTGGGCACTGACACCTTGATTTTCAAATTATTGGGGTTTTGTTCTGGTTTTGAGACAGGTTTTCTCTGATTCACGACCTCCATGAAGAGTGAGTCCCTCTCTATGCTTGTCTCCTCTGTAGCAGTGGTTTAAACAAAACACCTCAGAGGACCACTCCACTTCGTGAGGTTGTTTCTCATAGACTTTAAGTCTTGTCTGTGTTCATGAGCATAGGTCAGAGACCATTTAGAGTCTAAGTTAAGTCTAAAACTTAACATTGCTTTACAGGATTACCTAAAATTTATAAAATTAGCAAAAACCATACTGCTTTGGAAGTGGATGTGTGGCTTTCATTAAGTGGGAACTATTAATATTTAATTGTGTGAAACAAAAGGAATTAGTATGTATCATTTTCCTTGTTTACATATTTAATATGAACTGAAGTAGCTCTATATAAGAATCCCTATCTTAGCATTTTTTTTTCCTCTAATAACATCCAAGGAATGTTTAATAACCAACGGTTGGGCTTTGGAGCAAAGTATCAGTTTTAAAACCTCGTGAGATGTTTTTGTGTGACTGAATTCCACATCTACTTTAGAATCTTTTTACAGTGTCAGTTTTCAGGATTAACTTTAATTGTAATTGTGTTGAATGTCTTTGCAG
Seq C2 exon
GGTAACTGGGATACTTCTGGCAGTGAACTGAGTGAAGGGGAATTGGAAAAGCGCAGAAGAACCCTTTTGGAGCAACTGGATGATGATCAATAAATTATACCAAATATATGTTTATAGTATGATTTAAAGTCTAATTCAGACCAGGGATTATTTTAAGTCCAATTTACATAACACTGGGTTTTAATTGTGTCACAGGAAAAAGTGCATTTATGTATTGTTATTGTGGACTTTATAAAAGCAAAGGAATTGAAAATAACTTGATTCTGTATCAAGAATCATATTTTCCTATGGTAATAACTGTCTTTCTGTGACCCTTTCACAGGGCACTACAGGATGGATTAAAAGTGGCAATTTCATGATAGCTGCAGACGTCTCTACTTTGTTCTAAGTCATGAGGTGATTTGATTTCCTTTATAGAAGTTGGATTTTGAAGATACAATGAAAATTTTTGATAATGTAGTACAAAAAAAGCACCAGCAACCTATGAGAAGACTGCTTTTTTGTGCACTACTGAACTGGTTAAAGCCAATGTGATCTTCTGTGGTGAGCTCTTAAGAAACAGGTGTTTTTGATGGAGCCTTGGTAGACCTTTAACAGCAGTGGTGCTAACGAGCACTGCTGTAAAAAAGCCACCATTATTTTTTATGAAACATCTGAACATTTTAAAAAGGCTTATGAGGGCATTATTTTGAGCATCTATTTTGAGGTGATGTTTTAAAATAGCTAACATCAAGTCAAATTGTAAATTAGTTGAAATATATTGCCTTAAGGACCTACTAAAGAATGTGCCACCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136-Prpf40a:NM_018785:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACCTAAGAAAAAGACTGGAAAGGA
R:
TGAAAGGGTCACAGAAAGACAGT
Band lengths:
349-1539
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: