BtaINT0110436 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014127 | PGHS-2
Description
Bos taurus prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) (PTGS2), mRNA. [Source:RefSeq mRNA;Acc:NM_174445]
Coordinates
chr16:69267473-69268337:-
Coord C1 exon
chr16:69268156-69268337
Coord A exon
chr16:69267557-69268155
Coord C2 exon
chr16:69267473-69267556
Length
599 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGA
5' ss Score
4.74
3' ss Seq
AATTTTCCATAATCTTCTAGGTG
3' ss Score
9.34
Exon sequences
Seq C1 exon
GGAGGAAAGAGCTTCCTGATTCAAAAGAAGTTGTGAAAAAAGTACTTCTAAGAAGAAAGTTCATTCCTGATCCCCAGGGCACAAATCTGATGTTTGCATTCTTTGCCCAGCACTTCACCCATCAATTTTTCAAGACAGATTTTGAACGAGGACCAGCTTTCACTAAGGGAAAGAACCATGGG
Seq A exon
GTGAGACAGAGTTAAATGAGAATTTGTAGCAAATCAAGTTCTATGTGTAAAAACCTTAATGGAGTTTCCATTTTATCTCACTGGTTGAATAAAAAAATACATAACACATACTTACATACGTATATACAGATTATTATTTGTAGTTTGACTCATATTTTTAGTTTAAAATATTGGATCTGCAAAAAAGTTGTCTTCAAAAAAATTTGTTACCTTGATTATGCTGCCTTAAATATTATAAGGTGAGATTTTTGCAGCATTATTATCTCTTGGGTTTCAGTGACATAGCTTCAATGAATAAGTATTTTATATCAAAACATTTTCTGCTGCTTTTTAAAAGAAATATCATATAATTAGAGTGAAAATTTCTTATACAGGTTCCATATGAGACACTAATAGGAGACATTTAGATTTATAAGCTATGGGGTTATTTTTAGTGGATAAGCAAGTTAATTTATTATTTTGTGGCTGTGAAAAAAAATGTGTTACTGAAAATTTTAAAGCAAACTACATCATCACATTATCTAGTAATAAATACATCCTAGGCATTTTACATAAGAACAACTTCAGTAGCAAATCAAAAATTTTCCATAATCTTCTAG
Seq C2 exon
GTGGACTTAAGTCACATTTATGGTGAATCTTTAGAGAGACAGCATAAGCTGCGCCTTTTCAAGGATGGAAAAATGAAATATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014127:ENSBTAT00000018774:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0309810=An_peroxidase=PD(67.4=95.1),PF0309810=An_peroxidase=PU(3.0=18.0)
A:
NA
C2:
PF0309810=An_peroxidase=FE(7.3=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:
GAAAGAGCTTCCTGATTCAAAAGA
R:
TGCTGTCTCTCTAAAGATTCACCA
Band lengths:
222-821
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development