MmuINT0127122 @ mm9
Intron Retention
Gene
ENSMUSG00000061136 | Prpf40a
Description
PRP40 pre-mRNA processing factor 40 homolog A (yeast) [Source:MGI Symbol;Acc:MGI:1860512]
Coordinates
chr2:53018592-53019920:-
Coord C1 exon
chr2:53019810-53019920
Coord A exon
chr2:53018713-53019809
Coord C2 exon
chr2:53018592-53018712
Length
1097 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
AAGCTTTTTCCCTTCTTTAGCAA
3' ss Score
6.12
Exon sequences
Seq C1 exon
AAATCAATGTGGACAGAACATAAATCACCTGATGGAAGGACTTATTATTACAATACTGAAACAAAACAGTCTACCTGGGAAAAGCCAGATGATCTTAAAACACCTGCTGAG
Seq A exon
GTAAATGTTTGAAGACTAGGAATCAGAACTGTTAAGTAGCTTGGGTATAATTTTATATTAAGCTCCAAAGAACAGTTCTTCTGTGTCTCTAATTATTTAGGACATTGGGTGGAGAGGGCTAATGTAGTTAGAATAATAAGCAAGAAGAATAAAATTTGTTTTCCTATATGAACATACTTTGTTTAGTATCGTCCTATGTTCAAAGGTATCTTCAAGAATAAATTGAAGAGTAAGCAGTTTTCTTCAGTACAGGATGACCTGTATGGTTTTAAAAGACATGTTAACAGTTCCAGTTAACCATGGAGTTTGATATATTGAAATTAAATAATCTAAAAAATACTGTCTTGACTTAGAGTGGAATATTTTCTCTTTGTCAAGATGCCTCTGAAAGCATATTATTTTGTACTATACACTTTAACATCCAAAATCTATAAATATGATAAAAATAAAATTGAAGCAATAAATTAAGCAATATTGCCTGTCTTAATAGTCATGCTCAGAAAGAGATGATCTTTTTCACTGAAGAATGGTTTACCTAGCCAGTGGTATTTCATTTTTATTTCCCTTACCTAAAGATGGTAAAGTGTTTTCCACACACTGTAGTACCCTGTAGTCTAATATGTACATAGTGTTTGAGAAGGAAGGGTGATAGGTAACATTTATTTCTCATTCAGATATACACTCTCTCAGAGTTACAACAAATTAATTGACTATGAAACTAAAGCATTAGGATAGATGAATCAGGTTTCACTTTTCCCCAAACTTTCTATTTGTCTTATTTGTATTAAATATGAATACTCCATTCAGTAATTATGGCTGATGGTTTTTAATATGTGAATGTAAGAGGGGATGTACACACAGTTGAAATTCAAGTAGATGCCTAACTTTAAGGAAGCATCATTGCACTTCCTAAATATATTATCTTTGACAAATTATTTTCTCTTCAATAGTTAAATCATATATTCAGTAGTCGACAGCTCTCATGCTATGAATGTATGTAGAGTTTCATAGGTAGACAATGTCTGGTAAAAACAAGTGCAGATAATCAGCAGTGCTGAATATGTTACTATTTGCTGAAAGCTTTTTCCCTTCTTTAG
Seq C2 exon
CAACTATTGTCTAAATGCCCATGGAAAGAGTACAAATCTGATTCCGGGAAGCCTTATTACTATAATTCTCAAACAAAGGAGTCCCGCTGGGCCAAACCTAAGGAACTTGAAGATCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061136-Prpf40a:NM_018785:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.775 A=NA C2=0.561
Domain overlap (PFAM):
C1:
PF0039721=WW=PD(93.3=75.7)
A:
NA
C2:
PF0039721=WW=WD(100=73.2)
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:
ATCAATGTGGACAGAACATAAATCAC
R:
CTTCAAGATCTTCAAGTTCCTTAGGT
Band lengths:
230-1327
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: