HsaINT0133979 @ hg19
Intron Retention
Gene
ENSG00000107317 | PTGDS
Description
prostaglandin D2 synthase 21kDa (brain) [Source:HGNC Symbol;Acc:9592]
Coordinates
chr9:139873445-139873751:+
Coord C1 exon
chr9:139873445-139873584
Coord A exon
chr9:139873585-139873674
Coord C2 exon
chr9:139873675-139873751
Length
90 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
CTGAGGTCACCCACCTACAGGAA
3' ss Score
6.15
Exon sequences
Seq C1 exon
TTCCTGGGGCGCTGGTTCAGCGCGGGCCTCGCCTCCAACTCGAGCTGGCTCCGGGAGAAGAAGGCGGCGTTGTCCATGTGCAAGTCTGTGGTGGCCCCTGCCACGGATGGTGGCCTCAACCTGACCTCCACCTTCCTCAG
Seq A exon
GTGGGACAGCGGGCAGGTGGGTTTCTGGGACGGAGAGGTCCAGGGACACCCTCGGGCCTAACCCCTGACCCTGAGGTCACCCACCTACAG
Seq C2 exon
GAAAAACCAGTGTGAGACCCGAACCATGCTGCTGCAGCCCGCGGGGTCCCTCGGCTCCTACAGCTACCGGAGTCCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107317-PTGDS:NM_000954:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.210
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=PU(56.2=95.7)
A:
NA
C2:
PF0006118=Lipocalin=PD(42.5=55.7),PF0006118=Lipocalin=PU(13.6=13.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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:
CTGGCTCCGGGAGAAGAAGG
R:
GGACTCCGGTAGCTGTAGGAG
Band lengths:
171-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)