MmuINT0170914 @ mm10
Intron Retention
Gene
ENSMUSG00000020407 | Upp1
Description
uridine phosphorylase 1 [Source:MGI Symbol;Acc:MGI:1097668]
Coordinates
chr11:9135164-9136164:+
Coord C1 exon
chr11:9135164-9135310
Coord A exon
chr11:9135311-9135960
Coord C2 exon
chr11:9135961-9136164
Length
650 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGC
5' ss Score
10.4
3' ss Seq
AGGCCATTGTTTTTTTGCAGCGG
3' ss Score
7.49
Exon sequences
Seq C1 exon
GGCAAGGCCGTCTGGATGGCGCCCTCTGCTCCTACACAGAGAAAGACAAACAGTCTTATCTGCGTGCAGCCCATGCCGCGGGTGTCCGAAATATCGAGATGGAATCTTCGGTGTTTGCCACCATGTGCAGTGCCTGTGGCCTGAAAG
Seq A exon
GTACGCCGATATGGCATGGCCTTGCTGTCCTTTCTCTGTCTCTTTTGCTGGACCATCATGGAGGGGTCCTCCTGAGAGTACCCCAATGCTGAATTCTCAGTTTCTGACCAAGGCGTCATTCCTGTAGTCCGGGTACACATACGATGAGTTGACTGTCACACAGAAAAGCACGGATCCTGAGTGTTCTTGCAGATTCCACTGAGAGGGGTCAGAAAGACGGTGATGGGATTTCATGCTGCCCAGGAAGCTGCTCCAGCCCTGCTGACAGCTTGGCTTTCTGAAGGGCTAATCCACCCTGTTATCTAGTCCTGAACATCCTTCCAGTTCAGCATTAGCCCTCAGAACTGCCTGTGCTCCATGGGACAACGTATGCCCTCAGTCCTGCACAGGGCAGCCAGGTGCTGGCCCTGGAAACAGCTGGAATGTTTTGGGACCCAAGGGCAAAGGCATAGGTGATAGAGCTGGACTCTGCCAGAGTTGCTGGAAGTTCCACTCTGTCCACACAGCACTCCCAACTGTCCCTAGCCTGCACACTGCTGGTTTCCCGAGGTATTGCAGGCTGATCCTCAGCTCCAGAGCCCTGGCCTTCCTCCTTGGTGAGCTAAGGAAGGTATCCATCCTGCATTGATGAGGCCATTGTTTTTTTGCAG
Seq C2 exon
CGGCTGTGGTGTGTGTCACCCTTCTGGACCGTCTGCAAGGAGACCAGATCAACACTCCCCACGATGTGCTTGTGGAATACCAGCAGAGACCACAGCGGCTAGTGGGCCACTTCATCAAGAAGAGCCTGGGACGGGCCTGAGCCCTGTGCCTTTCCGCCCCGGAGAAGCCTCTGCAACTCCTGGGCAATAAATCTATTTTTTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020407:ENSMUST00000020677:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0104815=PNP_UDP_1=FE(19.5=100)
A:
NA
C2:
PF0104815=PNP_UDP_1=PD(15.5=83.0)
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:
GGCAAGGCCGTCTGGATG
R:
TAGATTTATTGCCCAGGAGTTGCA
Band lengths:
342-992
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types