HsaINT0133983 @ hg19
Intron Retention
Gene
ENSG00000107317 | PTGDS
Description
prostaglandin D2 synthase 21kDa (brain) [Source:HGNC Symbol;Acc:9592]
Coordinates
chr9:139875285-139876194:+
Coord C1 exon
chr9:139875285-139875307
Coord A exon
chr9:139875308-139876030
Coord C2 exon
chr9:139876031-139876194
Length
723 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGC
5' ss Score
7.96
3' ss Seq
CTTTCGGTCACACCCCTCAGGAC
3' ss Score
7.09
Exon sequences
Seq C1 exon
ATAAGTGCATGACGGAACAATAG
Seq A exon
GTGAGCCACTCCATTCATTCATTCATTCATTCATTCATTCATTCATTCAACACACATCCACCCAACCCACTCTGCGATGGGATGGATCAGGGCCCCAGGACAGCCTGGTGCTGCAGACCCATCCTTCCCGATGGCTGCAGTCCAGGGCCGGGCGGGAGACACTGGGGCTGCCCACATTGATGGGTGCACAGGTGTGAGGCTCAGAAGGAAAACCTGTCCCAGTGGCTGGAACAGGGCTGACTCCTGAAGGCTCATGGTTGGGGGGTGCAGGTGCGAGGCCCCAGGCAGACAAGGCCAAGGGGCTATACCACAGGGACCACCTGGCAGCAAGGGTGTCTGGCTCCTGGGCTAGGAGGAAACCAGGGTGGGGGAGACAGGATGGGAGGGAACAGGGGATGGAAGGGGAGGGCCAAGGACGCTACATGGATGCCGTGGGACAGCTCGGAGAGCAGGCTCAGGGCGGATTCACCCACCACCCCCAGGAGGGAGGCCTAGGCTGGAGCTGGAGTCTGTGGACCCTGGGGCTGGGAAGGGTGGAGTCTGTAGACCCTGGGGCAGCGGGGATCCAAGCCCCAGGGATGGATCTTGCTCTCTCAGCGGGGCTCAGTGGGGCTGGGGGCAGAGAAAAGTCCCCGTAGCCCGCACCTGCTCCATCGACTGGAGTGGAGGTGGGCTGGGGTAGACTGCAGTCCTCCATCCTAGCCTTTCGGTCACACCCCTCAG
Seq C2 exon
GACTCCCCAGGGCTGAAGCTGGGATCCCGGCCAGCCAGGTGACCCCCACGCTCTGGATGTCTCTGCTCTGTTCCTTCCCCGAGCCCCTGCCCCGGCTCCCCGCCAAAGCAACCCTGCCCACTCAGGCTTCATCCTGCACAATAAACTCCGGAAGCAAGTCAGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107317-PTGDS:NM_000954:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.398 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=PD(0.7=11.1)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping 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:
ATAAGTGCATGACGGAACAATAG
R:
ACTGACTTGCTTCCGGAGTTT
Band lengths:
186-909
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)