BtaINT0110432 @ 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
chr16:69270067-69271399:-
Coord C1 exon
chr16:69271238-69271399
Coord A exon
chr16:69270184-69271237
Coord C2 exon
chr16:69270067-69270183
Length
1054 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGTCTGTACTGTTTTTGTAGCAA
3' ss Score
7.07
Exon sequences
Seq C1 exon
TGAACGTCAGAGGACGCCCCGGAACTCCGCACCGCGCCTCCTCCGGCCCCGCAGCTCCGATCCGCGCACCTCCACGCCTCCGCCGGCCCCGCGCCCCGCCCGCAGCCGAGATGCTCGCCCGGGCCCTGCTGCTCTGCGCTGCCGTGGCGCTCAGCGGTGCAG
Seq A exon
GTGAGTGAGTTCCTGGCGCCTGTGCCCGGGATTCCGCGGCTCCGTCCACCCGGGCTGAGTTTCTGCTCAGACTTCTCCCGGGAACTCCAGGTGTTATAAATACTCCCAGAATTCAGAGGCCGAGTCCGGACGGATAGCCCCGCTTTGCCCTCAGCTCTGATCTTCATGGGCCAGTTATTGCACCCATCTTTTCTCATCTGCTAAATAGGAACGGGGATACTAATTTGCAGGTTGTCACAAGAAGATCTGATCAATATATGTGAGGTGCTTTTGTATAGCACCTAACTGCTATTGAATGAAAATAATTGTATTATACAATTTCCCTAGTTAGTGCTTTCCCGTCCCAGGGAATACCAGATTGTTTTTTTAAGATAAACAGAATAGCTTAAAAGCAAGCTGTTTTTATTTTGCAAATTTCTTTATAGTTGGTTTTTGTCGTTTTTTTTAATGTAAATTAAGTCACGCCACCTTAATACTGTAAATCATTCAATGATCTCTCCTGACACGTAGAATAAAACCCAAATTCCCATAAAACCCGAAGGATCTGCCTTCACCTTTTCTGAATTTAGCTTCCAGCTCTCCCTCTCCTGCTGTCAGGCATGCCTCAGGGCCTTTGCACTTGTTTTCCTCTCAACTTAGAATGTTCTTCCTCCAGATCTTTATCCAGCTTTATGACAGAGAAGAAAGAAGTAGGAAAAAAAAAAAACCCCAAAGTTTGATTAAAATACTTGATCTATTCACTTTAGTTTTGAAAGTCCTACTTTGAGCCTCTTCTAAAGGCTAATTTGAGCATCTAAAGTTTCTAAGAAAAATTTAGCAACATGATTTCCCTGGTGGAATATTCTGTTACCTTTATTTAGAAAAGGAAGTTGGTATTTCTACATTATAACCATTCTGTGAGGCAAGTCGGGGGGGAAAAAAAAAGTTTTCCCATGACTACCTGTATATTTCTTGAATTTTTTATTGTGAAGTTGACTCATAGTAAGTAAAGCAATTAAATGCTTAAGATTGACACTGAAAAATTATTCATTCACTGTCTGTACTGTTTTTGTAG
Seq C2 exon
CAAATCCTTGCTGTTCCCATCCATGCCAGAATCGAGGTGTATGTATGAGTGTAGGATTTGACCAGTATAAATGTGACTGTACCCGAACAGGATTCTACGGTGAAAACTGTACCACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014127:ENSBTAT00000018774:1
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:
PF0000822=EGF=WD(100=82.5)
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:
GAGGACGCCCCGGAACTC
R:
GTGTGGTACAGTTTTCACCGT
Band lengths:
270-1324
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development