HsaALTD0005144-2/2 @ hg38
Alternative 5'ss
Gene
ENSG00000095303 | PTGS1
Description
prostaglandin-endoperoxide synthase 1 [Source:HGNC Symbol;Acc:HGNC:9604]
Coordinates
chr9:122386446-122390345:+
Coord C1 exon
chr9:122386446-122386621
Coord A exon
chr9:122386622-122386732
Coord C2 exon
chr9:122390198-122390345
Length
111 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
3' ss Seq
CTGTGCTTCTCTCTCGGCAGATC
3' ss Score
12.5
Exon sequences
Seq C1 exon
GGGAGACCATCAAGATTGTCATCGAGGAGTACGTGCAGCAGCTGAGTGGCTATTTCCTGCAGCTGAAATTTGACCCAGAGCTGCTGTTCGGTGTCCAGTTCCAATACCGCAACCGCATTGCCATGGAGTTCAACCATCTCTACCACTGGCACCCCCTCATGCCTGACTCCTTCAAG
Seq A exon
GTGGGCTCCCAGGAGTACAGCTACGAGCAGTTCTTGTTCAACACCTCCATGTTGGTGGACTATGGGGTTGAGGCCCTGGTGGATGCCTTCTCTCGCCAGATTGCTGGCCGG
Seq C2 exon
ATCGGTGGGGGCAGGAACATGGACCACCACATCCTGCATGTGGCTGTGGATGTCATCAGGGAGTCTCGGGAGATGCGGCTGCAGCCCTTCAATGAGTACCGCAAGAGGTTTGGCATGAAACCCTACACCTCCTTCCAGGAGCTCGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000095303-21-23,22-23-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0309810=An_peroxidase=FE(30.1=100),PF0309810=An_peroxidase=PU(0.1=0.0)
A:
NA
C2:
PF0309810=An_peroxidase=PD(5.2=20.0),PF0309810=An_peroxidase=FE(32.7=100)
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGCAGCTGAGTGGCTATTT
R:
TTGCGGTACTCATTGAAGGGC
Band lengths:
246-357
Functional annotations
There are 1 annotated functions for this event
PMID: 15361066
The splice variant lacks amino acids 396-432, corresponding to the last 37 amino acids of exon 9, and cannot be detected as protein. These amino acids form a loop at one side of the peroxidase active site of the protein. When expressed in either COS-7 or Sf9 cells, abundant PG formation was observed with the full-length protein, whereas the spliced protein did not form any detectable product. Peroxidase activity was readily detected in microsomes prepared from COS-7 cells transfected with COX-1 but not with the splice variant.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Autistic and control brains
- Pre-implantation embryo development