MmuINT0120183 @ mm10
Intron Retention
Gene
ENSMUSG00000017453 | Pipox
Description
pipecolic acid oxidase [Source:MGI Symbol;Acc:MGI:1197006]
Coordinates
chr11:77882118-77882763:-
Coord C1 exon
chr11:77882617-77882763
Coord A exon
chr11:77882277-77882616
Coord C2 exon
chr11:77882118-77882276
Length
340 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TCAGTTGGGGGTGGGGGTAGATC
3' ss Score
-0.02
Exon sequences
Seq C1 exon
ACCCTTAGGATCAATGTGTGTTACTGGCGAGAGAAGGTCCCTGGGAGCTATGGTGTATCACAAGCTTTTCCATGCATCCTGGGTCTGGATCTGGCCCCCCACCACATCTATGGACTGCCAGCATCCGAGTACCCGGGGCTGATGAAG
Seq A exon
GTAAGGAGAAAAGTGGTGAAGGTAAGGAGAAAAGACTAAGAAAGCTACTGAACTACTAAGTGCCCATGGAGGTCTTGGTATCCATGCTAACATCCCTCTCTAGGACCCTCCTGGAGTCTGTTTCACTATTGGCCACCTGCAGCACAAGCTCTTAAACACAGGGCAGGGCTGGAGACGAGGGCTAGGTAACTTTAGATGCTAACAATAGCTAGTACATGCCAGGATTGGAGATTGGGATGATGGGTGGGCACGTCCTGTATCCAAACCCACCCCTCACCGGCTGGTATGCCCAGAAAGCCAGCTTTACAGCTCATGCTCATTCAGTTGGGGGTGGGGGTAG
Seq C2 exon
ATCTGCTATCACCATGGTGACAATGTGGACCCAGAGGAGCGGGACTGCCCCAAAACCTTCTCAGACATCCAAGACGTTCAAATTCTATGCCACTTTGTCAGAGATCATTTACCAGGCCTGCGGGCTGAGCCAGACATCATGGAACGCTGCATGTACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017453:ENSMUST00000017597:5
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=0.038
Domain overlap (PFAM):
C1:
PF0126619=DAO=FE(13.5=100)
A:
NA
C2:
PF0126619=DAO=FE(14.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTAGGATCAATGTGTGTTACTGGCG
R:
CGTGTACATGCAGCGTTCCAT
Band lengths:
302-642
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