MmuINT0137257 @ mm9
Intron Retention
Gene
ENSMUSG00000041199 | Rpusd1
Description
RNA pseudouridylate synthase domain containing 1 [Source:MGI Symbol;Acc:MGI:1919186]
Coordinates
chr17:25864696-25865336:+
Coord C1 exon
chr17:25864696-25864792
Coord A exon
chr17:25864793-25865147
Coord C2 exon
chr17:25865148-25865336
Length
355 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TCACTCCCACCTGCGTGCAGCCC
3' ss Score
7.33
Exon sequences
Seq C1 exon
GCGCGCCAGCCAGGCCAAGACCTGGTTCCTAGTATAGGGAAGCGAGGTTGGATGCAGAGCTGAGAATTGACATCCTGGTCCCTTGGCCCTGTTGCAG
Seq A exon
GTAAGTCCTAAAGGGTCTGCCTGTGGTCACAGGCTGGTGGGAGGCAAGTTAGGGAGCGCTTGAAGTCCTGGGTGGTCCTGGGCAATAACCTAGCGTGAAGTGTGTAGGCGTGAGCTGGACAACCAGGCTGTTTATTCCACTTCAAGTCAGGGAGAGCTCCCTAACCCTGAGTCCATGGCAAGTCAGAATCACCTGACCTTGGCCAGACTCCCATTCCGGAGCTGACACCCCTGGCATGGGCCCTTGTGGAAGACATAAAGGGTTCCAGCAGGTTCTGGCCCCAGTAAGTGTGTACAGTACTTGAAGACCAGGTCAGGCACCCTCCTACCCCAGGCTCACTCCCACCTGCGTGCAG
Seq C2 exon
CCCCACCATGGAGCCTGGCAGCATGGAAAATCTGTCCATCGTGTACCAGAGCAGCGACTTCCTGGTGGTGAACAAGCACTGGGACCTGCGCATTGATAGCAAGACCTGGCGGGAGACCCTGACCCTACAGAAGCAGCTCCGACACCACTTCCCAGAGCTGGCTGACCCTGACACCTGCTATGGGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041199-Rpusd1:NM_028009:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0160011=Corona_S1=PU(44.4=98.4),PF0084917=PseudoU_synth_2=PU(26.5=72.1)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCCAGGCCAAGACCTG
R:
GAACCCATAGCAGGTGTCAGG
Band lengths:
278-633
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: