MmuINT0128481 @ mm9
Intron Retention
Gene
ENSMUSG00000015090 | Ptgds
Description
prostaglandin D2 synthase (brain) [Source:MGI Symbol;Acc:MGI:99261]
Coordinates
chr2:25324353-25324647:-
Coord C1 exon
chr2:25324508-25324647
Coord A exon
chr2:25324430-25324507
Coord C2 exon
chr2:25324353-25324429
Length
78 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CAAGGGCAATCTACCCACAGGAA
3' ss Score
6.22
Exon sequences
Seq C1 exon
TTCCTGGGGCGCTGGTACAGCGCGGGCCTCGCCTCCAACTCAAGCTGGTTCCGGGAGAAGAAAGCTGTATTGTATATGTGCAAGACAGTGGTAGCCCCCTCCACAGAAGGCGGCCTCAATCTCACCTCTACCTTCCTCAG
Seq A exon
GTGAGACAAGGGGTTATGGCAAATTCTGGGAGACATCCTGGGGCTTGGTCCCTTACTTCAAGGGCAATCTACCCACAG
Seq C2 exon
GAAAAACCAGTGTGAGACCAAGATCATGGTACTGCAGCCTGCGGGGGCTCCTGGACACTACACCTACAGCAGCCCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015090-Ptgds:NM_008963:2
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=0.037
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=PU(31.0=95.7)
A:
NA
C2:
PF0006118=Lipocalin=FE(17.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCAACTCAAGCTGGTTCC
R:
TAGGTGTAGTGTCCAGGAGCC
Band lengths:
175-253
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: