MmuINT0128480 @ mm10
Intron Retention
Gene
ENSMUSG00000015090 | Ptgds
Description
prostaglandin D2 synthase (brain) [Source:MGI Symbol;Acc:MGI:99261]
Coordinates
chr2:25468988-25469734:-
Coord C1 exon
chr2:25469560-25469734
Coord A exon
chr2:25469128-25469559
Coord C2 exon
chr2:25468988-25469127
Length
432 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CAGGCATCCACTGGTCGCAGTTC
3' ss Score
1.1
Exon sequences
Seq C1 exon
TTTTCCTTGCTTTGTCCACATTGCTGGCATCAGGCCCAGGCACCTGCTCTGCTCTGAGCAAATGGCTGCTCTTCGCATGCTGTGGATGGGTTTGGTCCTCCTGGGTCTCTTGGGATTCCCACAGACCCCAGCCCAGGGCCATGACACAGTGCAGCCCAACTTTCAACAAGACAAG
Seq A exon
GTGAGAAGGCCCCCTACCCCACACCCAAAGAAGCAGAGCCCTCAGGCCAGAGCCAGGCTTTCTCTTACCAAAGAGGGTGTTCTGGGCACTGTCAGCCTGTGTGCTTGTGCATGGGAGCTAGCTGGAACCACCCTGGCACACAGCCTGGTTGGTCCACCTGACTCTGTCAGGAATGTGGTATGCTCTGATATAGTGGACTAGGATGAGGGCTGTGACAAAGACAAGGAGTTCAACACCCTGGGGAAAGAGGGGGGTCTCTGCTACCCACTCCTCCATGGGGCGATGAGCCAGCCTGCTAGAAAGGGAGGGGAGTGGAGAGAGAGGCATGCTGCTAGGACCTGTGTGGGGAGGAGTCAGAGGAGGGAAGACCAGCCCACCAGGGTCTGCCCATGAGGGGCTCATGGAGCAGACCCAGGCATCCACTGGTCGCAG
Seq C2 exon
TTCCTGGGGCGCTGGTACAGCGCGGGCCTCGCCTCCAACTCAAGCTGGTTCCGGGAGAAGAAAGCTGTATTGTATATGTGCAAGACAGTGGTAGCCCCCTCCACAGAAGGCGGCCTCAATCTCACCTCTACCTTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015090:ENSMUST00000114251:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.079 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006118=Lipocalin=PU(31.0=95.7)
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:
TCCTTGCTTTGTCCACATTGCT
R:
CTGAGGAAGGTAGAGGTGAGA
Band lengths:
312-744
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