HsaINT0133978 @ hg19
Intron Retention
Gene
ENSG00000107317 | PTGDS
Description
prostaglandin D2 synthase 21kDa (brain) [Source:HGNC Symbol;Acc:9592]
Coordinates
chr9:139871956-139873584:+
Coord C1 exon
chr9:139871956-139872144
Coord A exon
chr9:139872145-139873444
Coord C2 exon
chr9:139873445-139873584
Length
1300 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GTGGGGGTCGCTCGCCGCAGTTC
3' ss Score
3.41
Exon sequences
Seq C1 exon
GCTCCTCCTGCACACCTCCCTCGCTCTCCCACACCACTGGCACCAGGCCCCGGACACCCGCTCTGCTGCAGGAGAATGGCTACTCATCACACACTGTGGATGGGACTGGCCCTGCTGGGGGTGCTGGGCGACCTGCAGGCAGCACCGGAGGCCCAGGTCTCCGTGCAGCCCAACTTCCAGCAGGACAAG
Seq A exon
GTGAGGGGCTTTCCTGCGTCATCCCCAAGGGCTACAGGACCCTGTCAGGGGAAGGGCACTTTCCGGCTGGGTCTTCCCCCTGGGAGGAGTGAGCGAAGTCCCGCAGTGCCGGGCAGTGCCGGCCAGGGACTGAGCGGGCGCGCAGGAAGGAGGCTGGGTAGCCGCCCGAGGAGGCTGCCCGCGAGAAGCCCTCCCTGGGCACCGCGTCCCGTCTCCCCTGATGGGCCACGCAGACACCGGGCCACACACGCGCCCACGCCAGCCAGACACGTCCACCCCTGTGGGCACGCGACCCCCAGAGGACACACGAGCGCACGTTCCACACCTGGGTGCCAGGACACGGGCGGGTGGGGCACAGGGATGGCGACAAACACTCCGTGCGCGGTGGGGGTTGGGAGGGACGCGCACCGCACAGACAGCCGGCGACGCGCGCTCTCGCCCGGGAGCTGCTCGGGGAAGCGCCGGAGCGCGGGTCCCCGCGCCGCGCGCCCCTCCCTGGCGTCGAGGAGAACCCCAGCGGTCCGCAGAGCTGAGCCGAAGACCCGCCCCGATCCCCGCCAGGAATGCGACGTCCTCTGCCGCCCGCTGTATGGGCCAGGCGCTCAGCCAGGGCACAGAATCGGGACCGGGGGCGGAGGGGCCGAAGCTGGCTGGTGGGCGGCGTGCGAGGGTGAGGGACTGTCCTCGGGAGGGGCGTGGCCAGACGGGGGTGCTGGGTGTCAGGGGCGTGGCCAGCTTCTGGGGCTGAGGCGTGAGGGGCGGGGCCATCTCCGGGGGAGGGGGAAGTGGGGCGTGGTCATCTCCTGGGGCGGGGCGTGAGGGGCGGGGCCACCTCCCGGGGCGGGGCGGGGGCCTGATGGGCGTGGTCAGCTCCTGGGGCGGGGACGTGAGGGGCGGGGTCAGCTCCTAGGGGGGCATGGGGCGTGAGGGGCGCGGTCAGTTCCCTGGTTGTGGACATGAAGGGCGGGGCCAGCTCTTGGGGCGGGGTCGTGAGGGGCGTGGTCAGCTCCTGGGGCGGGGATGTGAGGGGCGGGGTCATCTCCTGGGGCGGGGATGTGAGGGGCGTGGTCAGCTCCTGGGGCGGAGATGTGAGGGGCGGGGTCATCTCCTGGGGCGGGGATTGAGGGGCGGGGGTCAGTTCCTGGGGCGGGGCGTGAGGGGCGTGGCTGCTCGGGGGATTGGGCGTGGGGGCGGGGCCGGGTTGGAGACCGGAGGAGTAGACGGCAGAGGCGCCCCCGCAGGTAGGCGCAGGTGGGTCCGGAGGGTCCTGGCCGACGCGGGTGGGGGTCGCTCGCCGCAG
Seq C2 exon
TTCCTGGGGCGCTGGTTCAGCGCGGGCCTCGCCTCCAACTCGAGCTGGCTCCGGGAGAAGAAGGCGGCGTTGTCCATGTGCAAGTCTGTGGTGGCCCCTGCCACGGATGGTGGCCTCAACCTGACCTCCACCTTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107317-PTGDS:NM_000954:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.021
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006118=Lipocalin=PU(56.2=95.7)
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:
CTCCTCCTGCACACCTCCC
R:
GAGGAAGGTGGAGGTCAGGTT
Band lengths:
326-1626
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)