BtaINT0110435 @ 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
chr16:69268156-69269129:-
Coord C1 exon
chr16:69268986-69269129
Coord A exon
chr16:69268338-69268985
Coord C2 exon
chr16:69268156-69268337
Length
648 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GGCTTTCTCATTTTTTATAGGGA
3' ss Score
8.59
Exon sequences
Seq C1 exon
CGAGATCACATTTGATTGAGAGTCCACCAACTTATAATGTGCACTACAGCTATAAAAGCTGGGAAGCCTTTTCTAACCTGTCTTATTATACCAGAGCTCTTCCTCCTGTGCCTGATGACTGCCCAACACCCATGGGTGTGAAAG
Seq A exon
GTGAGTGAGAGGAGACAGAGTTATATTAACTGTAACTGGGATTGGATTGATACCTAGAAATTTTGATCCCAAACTATGATTATTTGTTAATAAAACCATTTTTTCCCTTCTTATGTATATCTCTGGATATTTTTTGAAATTGTGAGTCCATGTAAACTATTCCATGGAAGGAAATAGGCATTTTGGTATGAAAAAGTGAAAATGTTAGTCACTCAATTGTGTCTGATTCTTTGCGACCCCGTGGACTGTGGATAGCCAGGCTTCTATGTCCATGGAATTCTTCAGGCAAGAGTACTTGAGTAGGTTGCCATTCTTTTCTCTAGAGTATCTTCCTAACCTAGGTATCGAATCTGGGTCTTCTGCTTTGCAGGCAGATTCTTTATCATCTGAGCCACCAGGGAAGCCCAGACATTTTGGTATAATGTCATATGTTCTCAAATTCTTTCATTAAAACTGAATTGATACTAGTTAAAGTAGATTATTCAGTAAGAGGCTGTTCCCCTATATCTTAGAACTTCCATTAATATGATCCTGTTCAAAGTTGTATTTTTCCTGTAAGTGAAGAAGACCCTAGTAAATTGACAGTTCACTCTCCGCTTCCTTAAATATATAGATGGGTTCTTATTTTGGCTTTCTCATTTTTTATAG
Seq C2 exon
GGAGGAAAGAGCTTCCTGATTCAAAAGAAGTTGTGAAAAAAGTACTTCTAAGAAGAAAGTTCATTCCTGATCCCCAGGGCACAAATCTGATGTTTGCATTCTTTGCCCAGCACTTCACCCATCAATTTTTCAAGACAGATTTTGAACGAGGACCAGCTTTCACTAAGGGAAAGAACCATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014127:ENSBTAT00000018774:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.163 A=NA C2=0.033
Domain overlap (PFAM):
C1:
PF0309810=An_peroxidase=PU(31.4=55.1)
A:
NA
C2:
PF0309810=An_peroxidase=PD(67.4=95.1),PF0309810=An_peroxidase=PU(3.0=18.0)
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:
CGAGATCACATTTGATTGAGAGTCCA
R:
CCCATGGTTCTTTCCCTTAGTGA
Band lengths:
326-974
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development