BtaINT0119659 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006716 | PTGS1
Description
Bos taurus prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase) (PTGS1), mRNA. [Source:RefSeq mRNA;Acc:NM_001105323]
Coordinates
chr11:93219287-93219511:+
Coord C1 exon
chr11:93219287-93219327
Coord A exon
chr11:93219328-93219421
Coord C2 exon
chr11:93219422-93219511
Length
94 bp
Sequences
Splice sites
5' ss Seq
GCCGTAAGT
5' ss Score
10.11
3' ss Seq
TCAACTCTCTCCCTTCGCAGGGC
3' ss Score
11.45
Exon sequences
Seq C1 exon
GTCTGTCTCCAGCACGCAACGGCCACCCTGCACCATGAGCC
Seq A exon
GTAAGTCCGGCCCCAGTGCCCCCCGTTTTCCCCTGTGGCCTCCCGGTGGGGCTTTGAATGCCAGGCTCAGCCCTTCAACTCTCTCCCTTCGCAG
Seq C2 exon
GGCAGGGTATCTCGCTCCGATTCCCGCTGCTTCTCCTGCTGCTGTCGCCGTCCCCCGTCTTGCCAGCGGACCCCGGGGCGCCCGCGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006716:ENSBTAT00000008833:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTGTCTCCAGCACGCAAC
R:
GACAGCAGCAGGAGAAGCAG
Band lengths:
87-181
Functional annotations
There are 1 annotated functions for this event
PMID: 12242329
Comparison of canine COX-3 (with IR) activity with murine COX-1 and -2 demonstrates that this enzyme is selectively inhibited by analgesic/antipyretic drugs such as acetaminophen, phenacetin, antipyrine, and dipyrone, and is potently inhibited by some nonsteroidal antiinflammatory drugs. [in Stamm et al, wrongly cataloged as soluble variant]
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development