DreINT0121677 @ danRer10
Intron Retention
Gene
ENSDARG00000010276 | ptgs2b
Description
prostaglandin-endoperoxide synthase 2b [Source:ZFIN;Acc:ZDB-GENE-041014-323]
Coordinates
chr20:34224170-34224536:-
Coord C1 exon
chr20:34224424-34224536
Coord A exon
chr20:34224287-34224423
Coord C2 exon
chr20:34224170-34224286
Length
137 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
TATTTATTTTTGTGGTGCAGCGA
3' ss Score
6.94
Exon sequences
Seq C1 exon
ATTCAATACTCTGAACTGGCGAGGTACGACTCGAGACATCAAACACGCCACTGGAATGAAAAGTTCGGTATTATTTATTTTTTTGCTTCTGGGCTTCGTGGTTTGCACAGGAG
Seq A exon
GTAAGCCTACTAATTTCTTGTTTTTCTTTCATATTTATATCTAGCCTGTTATATTTTATGAACTATATGTTATATCATTGTTGTTGGCATATTATAAAACTGATGTATTTACTTATTTATTTATTTTTGTGGTGCAG
Seq C2 exon
CGAACCCTTGTTGCTCCCATCCCTGTCAGAATCGAGGTGTCTGTACGGAAATGGGCTCCGACGCGTATGAATGTGACTGTACACGGACTGGATATTACGGTCAAAACTGCACAACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000010276:ENSDART00000010028:1
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:
CAATACTCTGAACTGGCGAGGT
R:
GTGTTGTGCAGTTTTGACCGT
Band lengths:
227-364
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]