MmuINT0128482 @ mm10
Intron Retention
Gene
ENSMUSG00000015090 | Ptgds
Description
prostaglandin D2 synthase (brain) [Source:MGI Symbol;Acc:MGI:99261]
Coordinates
chr2:25468072-25468909:-
Coord C1 exon
chr2:25468833-25468909
Coord A exon
chr2:25468189-25468832
Coord C2 exon
chr2:25468072-25468188
Length
644 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
GTCATTTCTTGGGTTCCCAGACT
3' ss Score
6.18
Exon sequences
Seq C1 exon
GAAAAACCAGTGTGAGACCAAGATCATGGTACTGCAGCCTGCGGGGGCTCCTGGACACTACACCTACAGCAGCCCCC
Seq A exon
GTGAGTGAGCCACTTCCTTATCTGGGTACAACCCTCTGTCCCAAAATTGTGGGGATAATGGTCACAGCACATCCAAGGCCAGGTCTGATTGTGAGTCTGCCTCAGGCACACGGGGCCACCTCTCTCTGGGGACTTTAGCCTCTCTGAGGCCCACCCACATTCTTCAAGGTCCCTTTCCTGCCCAAATGGAATTTTCCAGTACTCTGCTGCTCAAGTGGGTCACATACAGGCATTCCCCAAATCCTACCCACATTTCATAGCTTCTATCCAAGGACCTCTTTCCACCCCTCACCTGAGCTCTGGCTCCCCACCAGAACCCTATTCCCTTTGCCTTCCGGCTATATTGTAACCCAGCCTGCTGATGTCTTCGGTCTAAGTGCTTTCTACTCTCTCCCTAAGACTTATGGTTTGGAGACAGTGTTCCCAGGCTGTTCAGGCAGGGAGCTAGAAACTGTCTGGTGGCCACCCGGGGGGGGGGGGGACGCGGGGGGGGGGGGACAGGGAGGGCAGCCAGAGCAGAGGTGGATGAAGAAGACCTGAGACCCCCCCCCACAGAGAAGCCCCCAAAGGCCACCCGCTCTGAGCAGAGGGACGGAGATGTGGGAGCCACATGTTCCAATCAGTGTCATTTCTTGGGTTCCCAG
Seq C2 exon
ACTCGGGCAGCATCCACTCCGTGTCAGTGGTGGAGGCCAACTATGACGAGTACGCTCTGCTATTCAGCAGAGGCACCAAGGGCCCAGGCCAGGACTTCCGCATGGCCACCCTCTACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015090:ENSMUST00000114251:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(17.9=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(26.9=100)
Main Inclusion Isoform:
NA
Other Inclusion 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:
AACCAGTGTGAGACCAAGATCA
R:
TGTAGAGGGTGGCCATGCG
Band lengths:
190-834
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