MmuINT0170911 @ mm9
Intron Retention
Gene
ENSMUSG00000020407 | Upp1
Description
uridine phosphorylase 1 [Source:MGI Symbol;Acc:MGI:1097668]
Coordinates
chr11:9031633-9033351:+
Coord C1 exon
chr11:9031633-9031791
Coord A exon
chr11:9031792-9033236
Coord C2 exon
chr11:9033237-9033351
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-Upp1:NM_001159401:5
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=0.000
Domain overlap (PFAM):
C1:
PF0104815=PNP_UDP_1=PU(51.0=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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: