MmuINT0127108 @ mm9
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
PRP40 pre-mRNA processing factor 40 homolog A (yeast) [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53005128-53009805:-
Coord C1 exon
chr2:53009672-53009805
Coord A exon
chr2:53005243-53009671
Coord C2 exon
chr2:53005128-53005242
Length
4429 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
CATGTGTTTGTCGCCCGCAGATC
3' ss Score
12.91
Exon sequences
Seq C1 exon
ACATGGATAAAGAAGATGCATTAATATGCTTTGAGGAACACATCCGGGCTTTAGAAAAGGAAGAAGAAGAAGAAAAACAGAAGACTTTGTTGAGAGAAAGGAGGAGGCAGCGTAAAAATAGGGAATCTTTTCAG
Seq A exon
GTAATAGAAAGATGCCTATTCTGCCTTAGGTCTGTATTATAGTCATAGGATGTCAAGAAGAATCAAAGCACTTCTGAGATACTTGTTTCTAGTTCATTACCTAGGCTTTGTGGATGCCCAGTATGTTGAACTCTTTAATTTTTATAATTTAGGTTTTGTTCTTGGACATTTGAGGCGAAGGAATATAGCAAGGTGAAGCAAACATTATTTAACTTGAGCATAAGGCTTTAGCTGAACAACATAGCATAAGGGCTAGGTGGAAACAAGACAAGTGATGGGTGCTTTGTAGCAGTTGATATTTGGTTCCTAAAGAATGTGCTGTACAGCTTAGACATGGAACATAGTTAATCCCTTTACGTGGGAGTTTAAAGTATGTTCTGTAATCAGTAGCTTTTTCACTTCTAGTGGTGGTCTTCCCATTACAAAGAAATGAATTTTTGCTGTTTAAATTTTTATGGGTTTTCTTTGAGATAGGGTCCTAGGTGAGCCAGGCTGTCCTCAGACTTGCTGTGTAGCCCAGACCACTTTTGTACTCTTGATCTTTTTGTTTCCACCTTTCAAGGGCAGGGATTACAGACAAGTGCCACAATGCCTGCCTAAGGTATTTTACCTGTATAACCTGTGTTTTGAAGCTGTTCTTAGTATATCATGTTTGTTGAATATATTCAGGTAAATAAAGAAACGGACTTGGTGAGATACTACTAAGTATAGAGCTAGAATTTAAAACTATACAGTCTTGGTTACAAACAGTCTTTAGTCTTATATTAAACTCTGTATTAGGGTACCAGCAAGGTTGCAGTGGCTTATATAAGCTTGTTACCTGGCATTAATAGTCTGTTTGATCTATTGTTATCATTTAGGGTGGTAGTTCTTAAAATTTCACTTGTGTTAGATTCATGTAAAAGACTTTTTAAAAAACAGTTTACCATGTCAAGTGGTTACTATCTATTGCAATCACAGCCGTTTAAACACTAATTTACCTTTGTTCTATGAAACTCGCTACTCTGGTAAGTTACTTTTTTAGTTCTATGTAGGATTATTCATGTGACTACTAAGAACACAGATTATTAAGTCTCTCCTTAAGATTTCATCCAGTAGATACAGGGTAGGTTTTAATATGTACTAATATTGATGCACTCATATGAATACCAGTGACTTCTAAAGTTGTTTCTGATTGCCTACTTAGTGGGATATATCATTCCTTTGACCTCATTTAGCATGGAAATGATTTCAAAGACCAGTCTTACTACTAAAGCCTATGTTCTGTTTACCTATTTTCATATTCAGTTTTTGAGAATTCAATCTAATTTTCATAGCTAGCTATAAAATAGGCTATCCCTAGTTTTAAGATAGTCAACTATGTGACAAGAAAGAAAGGCTTTTAGGAGAGCCATTAGACTTCTGCAGCTTGTATGCTTCAAGGCCTTTTTAAGATTTTGAGTTTACAATAGTTTAAATTTGAACTAGACATAAAACTAGAAATCTGGGTCATAGAAACTACGACAATATGATACAGAGTACCAAATGCTATTACTGCAGGCCACGAGATTCTAATTAAAGGCCATGTAGGCCTTTAGCTAAGTGTAAAATAGGCTTTAAATCAGATTGATATGCATATAGCATGTTTGTGTTTAAGGTTAAAATAAGTGGTTATTAAATCACTATGTTGGTACTCCTTAAGATATATATGTAATTCAGTAATTTTTTTAGTCCTATTTTACCTTTCAAATTTTCAAAGAATTATTTAGAACTGTAGTAAAATGAATTAAGTGAAACTGTCATTTCCAAAATTAATCATGAGTGGAAAGAACCTATTCAGTAATGTGGTTTGGTGATTACAGTCTTTTTCTTTTGATTTGATTTGATCTGTCAGTTAATACTTACATAATTAAGTTTGTTACATCTTTGCTAGGAACCTGGTGAATTGTTTGTTTGTTTTTTTTAAAGTCTTAAGTCCCATGTTTAATTTGTGTCAGCTGTAATAGAAAGGTTTGAGACAAGTCTTTAAATTGAACAAAGGAAAAATGTGTCACAGAGGGGAAAATGTTGTAAGACAAAAGTAGTGGTCCTCTGAGAATGAGCCCTAGATACAGAGTTACCATTACCTGAGAAGTTACAAAATGCAAATTACTAAACCCTAAAACAAACTTACTAACTAAGATTCTGGTGTGGAGTCTAATGCTATGTTGATTTTATCCTTCAGATGATTGACAAATCCTAAGGGACAGGAAAATCTACAAAATAACAAATAGTTAAAGTTTTTATAGTGTGGAGACTTAAAGATACTGTTTAGTGTGTTACTTAAGATACTTAGTAATCACTAGCATAGTAAAGAGAGTTAAAAGATTGACAAATAGTTGAACATTACAATTAGACTTGAGATATTTTGGTAAGGAAAACCTCAGGACTTCTGTGTTTTATGCTTTGGGATGGATGCAGTGGTTGCACACACTTTTAATCCTTGCACGCTGTTGACAGAAGCAGGTGGATCTCTAAGTGCTCACAGCCAGCCTGGTCTGTCCCCTTTCAAGATCCAGGACAGCCAAGGGTACATGATGAGATCATGTCTTAAAAAGAAAAAAAGGAAAAGAGTGTTTTATGGATAAGAGAAAAATAGTCAAGGGAGAAAATGAAGGAACAATTTAAAGATGAGGGCTATCTCTCAAAATCTATGAACGTTCATAATTCAAACACAGATATAAATAGTAACATAAAGAACAGTATTGGAGGGGAAAAACGGGAACAAGTAAGAAAAGATAATACTGAATTAAATCTGAGGTAGAGATCTTCAACCAAGGAAAATGCTGTTGGTGATCACTATTCAAGGGAAAGTAACACTGGTAATTAGTGAATACCAGCTTTAAAGAAGTTATCAACCCTCCTGTGACAATTTTTCAACTGGAAATCCACTATTAGGATGAGACTCAAAAATCAGTGACTTGAGTGAGATATTAACAAAAATATATGATAGAAAGGAGTACATTTAAAAACTCCAGGAAGGAGTTTTTAAACACTTTAAGACTGAAAAGCTTTAAAACCACCTTCGCCGCTTTTGTTGAAAGAGGGAAGTAGCAGTAGGATGTAGGTACATGTTACTCTATAACATTGCTGCCCAGTGTATCCTGTATATGCAACTTAAACATAACCAGTTTCACATTTAGCAATCTAGTTAAACCAATATTTAAAGGCATTCTCTAAACAAGCAGTAATAGATATTTTTAAAAATTTTTAAATTGAGTAAATTTAAAAATTTACTCTGTAAACCAGTCTGGACTTGAACTCACATAGATTGTCTTCCCTCTGACTTTCAAGTGCTGGGATTAAAAGCATGCATTGCCACCATCTGGCAGAAGATCATACTTTATACTAGCCGCAATGTTCAGAAACTGCCTTTTATTGATGGCTTTTTAAATTTTCATTGTAATTTTTTATATCATGTATATGTATGTTTTGCATGCATGTTTATATACATACTATAAGGGCATCATAACTCCTAGAACTGGAGTTTTAGACTGGTAAGCTGTCATTCAGGAACTGAACCTGGGTCCTCTGTAGAAGCAGTGTGAGTCTAAACTGCTGAGTCATCTGTTGCTCCCCAGGCCCAGTAGCTCCTATTGAACAGTGGAGCCCTAGGAATTACAGAACTAAGGACTGGAAGAAGACCAATAGACACTGATAGTACTGAAGCCCCAGTGTGCAGTCCTGACTGTCAGCCACAGGAAAGGAAATGGGTGGTATAGAATAGACAATTTTTTTTTAAAGACAGAATAAAGTTACAATAAGCCTTCTGTTTAAGGAAGGGAAATGGTTGGGAGATCACATAGTGATTTAAATCCTAACTTTCCCAGAAGCTTTGAGGAGAGTAGTACATAACTATATTTGATTTATTTTTTAAAGATTTGTTTTATGTATATGAGTATTCTACTAATTTGTATATACCATTCACTTGCCTGATGTCCACATCACCTGAAACTGAAGTTACAGGTGATCATGAGTCACCTTATGGATGTTGGGAACAGAACGTGGGTCCCATCTGCCCCAAACCAAGAGCCATCTCTTCAGGCCATTGTTTAAAATTAACCTAAATAAAAATATCTAAATGATGCTATTAAAAAAAAAAAGTTTTATACAGGACATGCACATACTCTTTAGCCTCATCATTTGAGAATAGATAATCCCAGTCATTTTAGTATCTTTGGTTTTTGGTTATATACATACACAATATTTTATGGATCTTGTTGTTTTTAACTGGAAGTGGCTTTCTGTCTTAAGGGATAGGTAACTGAAGACTAGAAGGATAGTATAGTCTTTTGAAAGATCTCTTTCTTTGGATGGCTTGTGTATATTATTTATTTGTGGTCTAGAAGTATTTTTGCTGGCACTTTTTACCATGTTTTTCTTGTATTTTACATGTGTTTGTCGCCCGCAG
Seq C2 exon
ATCTTTCTGGACGAGTTGCACGAGCATGGGCAGCTGCACTCTATGTCCTCTTGGATGGAGCTGTATCCCACCATCAGCTCTGACATTCGCTTCACTAACATGCTGGGTCAGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136-Prpf40a:NM_018785:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.267 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(23.2=28.9),PF0184614=FF=PU(10.7=13.3)
A:
NA
C2:
PF0184614=FF=FE(67.9=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: