BtaINT0110439 @ 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
chr16:69265899-69266830:-
Coord C1 exon
chr16:69266544-69266830
Coord A exon
chr16:69266047-69266543
Coord C2 exon
chr16:69265899-69266046
Length
497 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGC
5' ss Score
9.04
3' ss Seq
ATTTAATTCATATTCCACAGGTC
3' ss Score
9.07
Exon sequences
Seq C1 exon
GAGAAACTATTAAGATTGTGATTGAAGACTACGTACAGCACTTGAGTGGCTATCACTTCAAACTGAAGTTTGACCCAGAGCTGCTTTTCAACCAACAGTTCCAGTACCAGAACCGTATTGCTGCTGAGTTTAACACGCTCTACCACTGGCATCCCCTTCTGCCTGACGTCTTTCAGATTGATGGTCAGGAGTACAACTATCAGCAGTTTATCTATAACAACTCTGTCTTACTGGAACATGGTCTCACTCAGTTTGTTGAATCATTCACCAGGCAAAGGGCTGGCAGG
Seq A exon
GTAAGCATTATTAGTGAAAAATAAAATAAAACAAAGGACTGGTTGGTAACTAGAATGTCTGCTGCAGGAAAGATTTTTCTTAAACTTACTGAAAGATTAATTATTGCTAGTAATCTTTCCTTGAAATAAGAAGGCTGTGTAATATATATATTTAATATTATATGATCTTGATTATAATATAATTTTACCATTATAATCTAAATCATAGAAATAATCTATAAATATTCCAAACTTATAGTTTAGGTCTCCACTGGTAGCTTCAGTTTACCTACTTGGCACTCAAGGGATGTTTTTAAAATAGAAATCTTGGGAATTCCCTGGTGGTGCAGTGGTTAGAATTTCTTGCTCTCACTGCTGAGGGGCTGGGTTCAGTCCCTGGTCAGGGAACTAAAATCCCACAGGCCACTTAGCATGGCCAAAAAAAGAAAACAAAAAAAAATCTTACATATGCCTAAAACTCAATTAATGTGTTCTACAATTTAATTCATATTCCACAG
Seq C2 exon
GTCGCTGGCGGTAGGAATCTTCCAGTCGCAGTAGAGAAAGTATCAAAGGCTTCAATTGACCAGAGCAGAGAGATGAAATACCAGTCTTTTAATGAGTATCGCAAACGTTTTCTGCTGAAGCCCTATGAATCATTTGAGGAACTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014127:ENSBTAT00000018774:8
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(25.8=100)
A:
NA
C2:
PF0309810=An_peroxidase=FE(13.3=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:
TGAAGTTTGACCCAGAGCTGC
R:
AGGGCTTCAGCAGAAAACGTT
Band lengths:
348-845
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development