BtaINT0110440 @ 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
chr16:69263776-69266046:-
Coord C1 exon
chr16:69265899-69266046
Coord A exon
chr16:69265750-69265898
Coord C2 exon
chr16:69263776-69265749
Length
149 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
TGTCCTTGTCACCCTCACAGGAG
3' ss Score
9.21
Exon sequences
Seq C1 exon
GTCGCTGGCGGTAGGAATCTTCCAGTCGCAGTAGAGAAAGTATCAAAGGCTTCAATTGACCAGAGCAGAGAGATGAAATACCAGTCTTTTAATGAGTATCGCAAACGTTTTCTGCTGAAGCCCTATGAATCATTTGAGGAACTTACAG
Seq A exon
GTGGGAAACGGTTTCTAAACTCCTTCAAAGAGTCAAGGGGCAAATGGAAACAACAGAGAAATTGAAAGCAAATTGAGCGAAGGGGTAAAACTCCTCATTTTGTCAAAAGTTTGACATTGGTTGTATCTTTGTCCTTGTCACCCTCACAG
Seq C2 exon
GAGAGAAGGAAATGGCTGCAGAGTTAGAAGCGCTCTATGGAGACATAGATGCCATGGAGTTTTATCCCGCCCTTCTGGTAGAGAAGCCCCGTCCAGACGCCATCTTTGGGGAGACCATGGTAGAAGCTGGAGCACCATTCTCCCTGAAAGGACTTATGGGTAATCCTATATGCTCTCCCGAGTACTGGAAGCCTAGCACTTTCGGTGGAGAAGTAGGTTTTAAAATCATCAACACTGCCTCAATTCAGTCTCTCATCTGCAGTAACGTGAAAGGCTGTCCCTTTACCTCATTCAGTGTTCAAGATACGCACCTCACCAAAACGGTCACCATTAATGCAAGCTCTTCCCACTCTGGACTAGATGATATCAACCCCACAGTCCTACTAAAGGAACGTTCAACCGAACTGTAGAAGCCTAGCGATCATATTTATTTATTTATATGAACTGTTTCTTTTAACTTAATTATTTAATATTTATATGAAACTCCTTGTGTTACTTAACATCTTCTGTTAAGGAGAAAAAGGGGGTCATGCTTGTGAAGATTTTCATGTTGATTTTAAAGATGTCGAAGTTTCTTCAAGTTAAAGGGGAAAGCAGTTTTCATTCTTCTGTACAATCCAATGGGAAATGAGTATGACATTTTTTACTTGAATTTCAACTTATAATAAGAACAAAAGCTAAGTTTGAACATGTAAGTGCTGTTGCAAGATGACAAAATGCTGCACATTTCGACACTATCATATTTCCAGGGTGTCTCCTATGATGCCTGAGAAACAGCTGTCTACTCACTGGTCCTTTTCAGTCTCCTTTTAGCCATTTTCAGATCAGTTTACTTCGACTATTTTGTTTTCCTGGTTTTAAGGTCTGAGTGTGTTTTTTTGGACTCTGCCTGTACTTTCTTACCTGAACTTATGCAAGTTTTCAGGAAATCCTCAGCTCAAAACTACTACAAAAGGCCTTTACAAAAAGGTATACATTCATTTTAAGTGAAAGGCAAAGAACTTTACAAATAAACTATAACCTGATTAAGAGCCCAATACCTTAAAGCTCTAGGGGGTTCTCGACACCAAGAACGTATTCCTATTCTAATTAATGTCTTTCCTCATTTAAAAGCAAATAATTGCTGAATAGTTCCCAGGGAGACAATGCTTCTTTTCCACATCTCATTGTCAGTTGACATTTTCTGGTACTGTATATTAATTTATTGAGAGCTATTATGTCTTCTTAGGATGACTATTATAAACTGGGTTTAAGGCTACATGATGTTCTTTGTTGGCATTATGTCAGAATCAGTGTATCTTGTGGGATTACCTCTCCAAATTATTACTATAACATTAGTGTTTGGATTAAGATTTGTGAAAACATGTGAGGAATCCAACTCTGGTATACTGAGATGGAAAGTTGGAATTCGCCTTTAAGGCTTACCTACTCACCAGCCCACAGAGAACGTTGTCTCGTTACCCTGGATGTGCTGACACTGACAGTGTGTACGTTTTTGAAGGACTTGTGGATGTTTCATTAATTCATTCACCCCTAACTTCTGGAGAAACATTCTTTACAAAGCACTGTGGGTCTTAATATTTTTAAATCATGCACTGAAAATCAGTATTTATGTAAATAATTGAACAGGTATGCCTGTTAGGCAAAGGGAGAAAAATGAAATTTCATTAAAGAGAAATAACTCAGGGGAATTTTTAGGATTTTATGTTTAAATGATTTATGGTTAATAAAGAGTCAATAGTAGAAGAGCTTGTATTAAAAAAACTGTTACCTTCATTGATTTTTTTAAAAAACTGATTTGTTAAATATCTGAATGACTGAATCTGGGAATTTGGAATATATGAGTGTTTTGGTGCCTCAGACTATGGTTAAATTAATTTATGTAAACTGTAAGTGTTGAAACAAATAGCTGTTTATTTTTGTATTATTTAAAAATTGAAAACCTCTTCTAAAATAAATTTTGACTGTTTCTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014127:ENSBTAT00000018774:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0309810=An_peroxidase=FE(13.3=100)
A:
NA
C2:
PF0309810=An_peroxidase=PD(27.2=73.0)
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:
AACGTTTTCTGCTGAAGCCCT
R:
CCGAAAGTGCTAGGCTTCCAG
Band lengths:
250-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development