BtaINT0119666 @ 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
chr11:93229689-93231928:+
Coord C1 exon
chr11:93229689-93229772
Coord A exon
chr11:93229773-93231681
Coord C2 exon
chr11:93231682-93231928
Length
1909 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCA
5' ss Score
6.37
3' ss Seq
CAGGTGACTCCATCCCGCAGATG
3' ss Score
8.05
Exon sequences
Seq C1 exon
GTAGACCTCGGCCACATTTATGGAGACAATCTGGAACGTCAGTATCAGCTGCGGCTCTTTAAGGATGGGAAACTCAAGTACCAG
Seq A exon
GTAGCACTGGGCCTGGGGCTGGGGCATTGGGAAGGGCCTTCCACAGTCTCCCCTGGCAGAGGGTGTTGGTGGGGGGCCTTGGTGGTGTCCTATGGCGGAAGCTGTAGGTGCATGGGAGGAGAAGCGACAGTAAACCCTGGGAGCAGGTGCCAGGCAAGAGAAGCAGACAGGGAGCAGACGTGGGCTCTTGTGTTCTCTTGGGAGGTGGATTTTGGGGCTCCACAGAAAATGGACAGTTCCAGTCTGCATTTATTCGTTTAATCATTCCACAATATTAATTGGGCACTATGGTGTGCCGGGCAGGTGAGCAGTGGCCATGGTAGTTGTAAGCCCTGCCCTCAAGCCCACAGACACAAACCCTAAGGTGCTAGTTCCACGAGGACGTTTTGTCGGAACTCTCACTGTCCAGGAATGTGAGGGCCACATAGGTGATTATCTCATGCGCTCCTCAGATCTACTGCATAAACTAGGTACCATTTGCCCTCTTTTATAGACGTGAGTCACATCCAAGTTATTAAAATTTTTCTAGTGGTCACATTAAAAAATGTAAAAAGCAACAAGCAATATTGATTTTAATAATATATTTTTGAATTTAACCCAGTATATCCAGGATATCCTCATTTCAACATGTAATCAACACAAAAATTGTCAATATCTCATTTTTTGTGCTAAATCTTCACATTCTGACTCATATCTTACAGTACATCTCAATTTGGGTGCCAAGTTTTCATTGGCGATTCTGATCAGCATTTAGATTTCATAAAATTTTGCGGTTGAGAAAGTAGATTCACATGTTCAAGTTGTTCTAAGCATAAAGACTTTCCGATAGCTGGGATCTTGATTTAAAAACGTGAATCTAAAGTAAATGAAATTGAAAATCAAGCTCTTTATCCACATCAGCCACATTTCTAGTCCTCAGTAGCTGCACGTGGCTAGTGGCTCCCATTCTGGACCATGCAAATCGAAACAAAAACCGAGACGGGAGGTTCACTGCTGAATCTTTCGAGCTAAGAACAGTATCTGGCATATAGGAGGTCCTCTGTGTTTATTTACTGAGTGAATGAGGAAACTGCCATATGATTAATTACACCTGTGATAGCTGCCACAGGCAGAAGCCAGGAGAGTGTGCAGAGGCTGGGGAAGGCTTCCTTAGGAATTATGAATAAACCAAGAGTTGCATGAAGGATAAGGAGGAATCAAGGAGGCCAAGAAGGGCCCAGGGCTGTCCAGATTCTCAGGTTTCAAGGCTGGAGAGGGGCAGTCGCTTGAGTGACGTTGAGGCAGTGAAACAAGGGATATGCTGTTGGACATCTAATGAGCGTGGGTCGTATTAAGGATTTCTGATTTCTGCCAAGAGCAGAGAGAAGACTTGGAAGGTTCTTTAAGCCAGGATGTGATTCTAGATTTGGATGTTTTAAAGCAAGGGTCCCCTACCTTTTTGGTACCAGGGGCCAGTTTCAGGGAAGACTATTTTCCCATGGACTGGTGGGAGAAGGGATGGTTTCAGGATGATTTGAGCGCCTTATATTTGCTCTACATTTTATTTCTATTATTATTACATCAGCTCCACCTCAGCTCATCAGGCATTAGATCGTGGAGGTTGGGGACCCCTCTTTTAAAGCACTGCTCTGGCTGCAGAGCTGAGAACGTCTAGAGGAGAGAGTCACTTACAAGGGGAGTCGGGGTGGAAGATGAGGGTGGCTTGGAAGAGTGTGGTGGCCATGGGGAGAGAGAAAGGGACTCATGTTAGGAGAGCTTTAGGAGATAGAATCCACAGGCCTTGGTTAGGAAGGCCGGACAGCTGCCCTGCGAGTTACGGGCAGCTGTCAGTAGGAGTGGGCGGATGTCAGCGGTGCAGGTGCTGGTGCCCCGCCCCCTCCCCAGGTTACCAGGTGACTCCATCCCGCAG
Seq C2 exon
ATGCTCAATGGAGAGGTGTACCCGCCATCGGTGGAAGAGGCTCCCGTGCTGATGCACTACCCCCGGGGCATCCCGCCCCAGAGCCAGATGGCCGTGGGCCAGGAGGTGTTTGGGCTGCTTCCTGGGCTCATGGTCTACGCCACGATATGGCTGCGTGAGCACAACCGCGTGTGTGACCTGCTGAAGGCTGAGCACCCGACCTGGGGCGACGAGCAGCTCTTCCAGACGGCCCGCCTCATCCTCATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006716:ENSBTAT00000008833:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0309810=An_peroxidase=FE(6.1=100)
A:
NA
C2:
PF0309810=An_peroxidase=FE(18.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCTCGGCCACATTTATGGA
R:
GATGAGGATGAGGCGGGCC
Band lengths:
327-2236
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development