MmuINT0137259 @ mm9
Intron Retention
Gene
ENSMUSG00000041199 | Rpusd1
Description
RNA pseudouridylate synthase domain containing 1 [Source:MGI Symbol;Acc:MGI:1919186]
Coordinates
chr17:25865468-25865873:+
Coord C1 exon
chr17:25865468-25865591
Coord A exon
chr17:25865592-25865770
Coord C2 exon
chr17:25865771-25865873
Length
179 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
GTGATGTCCTTGCTCGACAGGTC
3' ss Score
10.15
Exon sequences
Seq C1 exon
GTTCTGCCACCAGCTGGACTTCTCCACCAGTGGGGCACTGTGCGTAGCCCTGAATAAGGCAGCTGCGGGCAGTGCTTATAAATGCTTCAAGGAACGGCGAGTCACCAAAGCCTACCTGGCACTG
Seq A exon
GTAAGTCCTGGCCAGTTCCTGGGATGCTGTGTGGAGACCCAAGGCTCACAGCCTACTCCAGCAGGCCTCTCAACTGAAGCTCCGTGCCAGGCTTATGTGCCTATCTAGAGCTCAGCCACATTCCTCTCAGAGATGACAGTGTGGCCCAGTGAGCTGCATGTGATGTCCTTGCTCGACAG
Seq C2 exon
GTCCGAGGCCATGTCCAGGAAAGCCAAGTGACGATCAACTATGCCATTGGCAGGAATAGCACGGAGGGGCGGACGCATACCATGTGCATCGAGGGCACTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041199-Rpusd1:NM_028009:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.086
Domain overlap (PFAM):
C1:
PF0160011=Corona_S1=FE(30.4=100),PF0084917=PseudoU_synth_2=FE(24.7=100)
A:
NA
C2:
PF0160011=Corona_S1=PD(23.7=91.4),PF0084917=PseudoU_synth_2=FE(20.5=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:
TTCTGCCACCAGCTGGACTTC
R:
CATGAGTGCCCTCGATGCA
Band lengths:
226-405
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: