MmuINT0128483 @ mm9
Intron Retention
Gene
ENSMUSG00000015090 | Ptgds
Description
prostaglandin D2 synthase (brain) [Source:MGI Symbol;Acc:MGI:99261]
Coordinates
chr2:25323338-25323708:-
Coord C1 exon
chr2:25323592-25323708
Coord A exon
chr2:25323440-25323591
Coord C2 exon
chr2:25323338-25323439
Length
152 bp
Sequences
Splice sites
5' ss Seq
ACAGTAGGT
5' ss Score
5.67
3' ss Seq
GACCGTTCTTTATCTACCAGGCA
3' ss Score
8.39
Exon sequences
Seq C1 exon
ACTCGGGCAGCATCCACTCCGTGTCAGTGGTGGAGGCCAACTATGACGAGTACGCTCTGCTATTCAGCAGAGGCACCAAGGGCCCAGGCCAGGACTTCCGCATGGCCACCCTCTACA
Seq A exon
GTAGGTATCCCAGCCCACAGGTCCACGCACAGGGGAGATGCCTGGGGTTGGAAACAGACCAAGACCTGACCCTAGAGAACAGTAACAAAGGTGTGTGGGAGCAGGGCGGGGGCTTTTTGCTTCCTGACACCAGACCGTTCTTTATCTACCAG
Seq C2 exon
GCAGAACCCAGACTCTGAAGGACGAGCTGAAGGAGAAATTCACCACCTTTAGCAAGGCCCAGGGCCTCACAGAGGAGGACATTGTTTTCCTGCCCCAACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015090-Ptgds:NM_008963:4
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:
PF0006118=Lipocalin=FE(26.9=100),PF0144313=Viral_helicase1=PU(47.4=90.0)
A:
NA
C2:
PF0006118=Lipocalin=FE(23.4=100),PF0144313=Viral_helicase1=FE(44.7=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:
ACTCGGGCAGCATCCACT
R:
CGGTTGGGGCAGGAAAACAAT
Band lengths:
218-370
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: