MmuINT0170911 @ mm10
Intron Retention
Gene
ENSMUSG00000020407 | Upp1
Description
uridine phosphorylase 1 [Source:MGI Symbol;Acc:MGI:1097668]
Coordinates
chr11:9131630-9133348:+
Coord C1 exon
chr11:9131630-9131788
Coord A exon
chr11:9131789-9133233
Coord C2 exon
chr11:9133234-9133348
Length
1445 bp
Sequences
Splice sites
5' ss Seq
AGCGTGAGT
5' ss Score
8.2
3' ss Seq
GCATTTCTCTCTGGTTTCAGCAT
3' ss Score
8.35
Exon sequences
Seq C1 exon
TTTGTGTGTGTTGGTGGAAGCTCTTCCCGGATGAACACCTTCATCAAGTATGTGGCTGCAGAGCTGGGCCTTGACCATCCAGGGAAGGAATATCCCAACATCTGTGCAGGCACTGACCGCTACGCCATGTATAAAGCCGGGCCCGTGCTGTCTGTGAGC
Seq A exon
GTGAGTACTTGCCTTTCACTTGGATTTGGTTGCCAGGCTCTGCAAGGCCCTGTGCCCCACACTTTTGCATATGGGAACAGCTGAACAGCTGGCACCCTAGTGTTTGTTTACTGTAAATGGCTGGGAGCTTGGTGAGCTCTCAGCAGCTGGGACCTGGGCATGAGTAAGTCCTAGGCTCCAGCTCTTGCGGCTTCACCTCCTGGAAAGCCTAGCTATACAAAAGCAGATACACATGCAAATATGCACAGCTGTCCACTCATTGTGGGGGTGGCAGTTCCCAGGAGGCCGAGGGCTGTTAGGAGCCACATACCAGGCATCTACGCTCTGTCTATCTCACAGTAACTGACCTACTTTATAACACAGATTGAATAAGTAATAAAAGTTAATATAGAAAAATCTCCAGTATCCTGTCAATGAGATGATTTTCTAGCTCTGATTTTGATTTGATGGCAACAGTATAATGATATATATCACATACTTGACATATATCATAAGGAGATAATAATATAGTGAAGAACTGTGGTTCAGAAGTGGATTCCCTTCCTGTTGATATTTTGCGTCTTGACCCTCGTCAGTTAAACATCCAAGTCATGTCGAATCGTCTGAAAGCAAGTACACCTTGTGGGAGCATTTTCTGTATCTGACATTCTGGAAGGGGTCCTTTTGCAATATGGCTTTGCCATAGGGACAGCTGTTCAGGGAGGGGATGGTGTCGTAGGAGATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTTTGGAAGGCATGTGGAGTGGGATTGCATTGCAGAGGCAAGGACGAAATGACAGAGGCAGAAGTACATACAGTTCAGGAACCATAGAGGTATCTTTGCTAAACTGGAGAGGGCATTTGAAAAATTCAGTGGTAAAACCTTATCCAGTATGGTGGCCTGTTTGCATGGCTTCAGATATCAGGGAAAAAGTTTGTTTCGTAATGACAGTAGCTACTTCCTTCCTGCTGCTATATAGATTGTACGAGTCAAATGAAGTCAGGTATAAGACAGCTCTGTTTATATTTTTGATGTCTGTCTTCCATTTCACATACTGATTTAATTGGTTGGAGTATACACATAACACATGCAGCACTCTCCTTCCACACGTGGGCTTTGTTTCAAAGACCCCCGTGGATGCCTCAAAGCAGGAGGGTATCAAAACTGGTAAATATGAATATTCCTTTTATAGAGACATTTTAGTGTGACAGTTAGGCATAGCAAAAGAATGGCAATAATGACTGACAAAGCAGAGTAATTTGAAGTAGAATATAGTAAAATATATGTGAATGTTCTTCCTCTCCGAAGCTCGTCTGTGCAAAGCTTAGTTGGGCCTGGGTGACTTGGAATGCAGAGCCTGTTGTTTGGAGGGCTTTGTGCATGCACTGACAGAGGAACAGTGGGCTGAGCCTCTGCATTTCTCTCTGGTTTCAG
Seq C2 exon
CATGGCATGGGCATTCCTTCCATCGGCATCATGTTGCACGAGCTCATCAAGATGCTGTACCATGCCAGGTGCTCCAACATCACCATCATCCGCATTGGCACTTCAGGCGGGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020407:ENSMUST00000020677:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0104815=PNP_UDP_1=PU(51.5=98.1)
A:
NA
C2:
PF0104815=PNP_UDP_1=PD(32.1=86.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGTGTGTTGGTGGAAGCTC
R:
TATCCCGCCTGAAGTGCCAAT
Band lengths:
271-1716
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