DreINT0121680 @ danRer10
Intron Retention
Gene
ENSDARG00000010276 | ptgs2b
Description
prostaglandin-endoperoxide synthase 2b [Source:ZFIN;Acc:ZDB-GENE-041014-323]
Coordinates
chr20:34222105-34222754:-
Coord C1 exon
chr20:34222611-34222754
Coord A exon
chr20:34222287-34222610
Coord C2 exon
chr20:34222105-34222286
Length
324 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GAATTCCCCTGTTTTGATAGGTA
3' ss Score
6.81
Exon sequences
Seq C1 exon
CACGTGCCCATCTGATCGATAGTCCTCCTACATTCAATGCTGACTATGGTTACAAAAGCTGGGAAGCCTACTCTAATCTCTCCTACTATACTCGCACATTACCTCCTGTCCCGCGTGATTGCCCAACGCCAATGGGAGTCGCAG
Seq A exon
GTGAGCCTCTTTCTCCTCAGACCTGTTTTCTCACATTTCTTAGCATTCACATTTACAACTGGACAGGAAGCTTGAGGTCACAAATAGCTCACTTGAGCCTTGGGTGTGTGGATAAGCAACTCATTAAAAGAAAGATAAGATGTGACAGTAATGAGTCATAGAGGCTAAAAAGTTTTAGACACTGTAGAGAGAATAAATGATTGCATAAATAGTTTTTGCACTTACAGTACCTGTAGATAGTGTTTCATGTTTGGGTTGGAGTATAAACTCAGACATGAGGATGGAAGTAGGCTCTGTTTCTCATGAATTCCCCTGTTTTGATAG
Seq C2 exon
GTAAGAAAGAGCTGCCAGACGTGAAGATGCTGGCAGAGAAACTGCTTCTTAGGAGGAAGTTCATCCCAGATCCTCAACGCACCAATCTTATGTTCGCTTTCTTCGCCCAACATTTTACTCACCAGTTCTTCAAATCTGACATGAAGAAAGGTCCAGCTTTCACAACAGCCCTGAACCATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000010276:ENSDART00000010028:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0309810=An_peroxidase=PU(31.3=53.1)
A:
NA
C2:
PF0309810=An_peroxidase=PD(67.5=91.8),PF0309810=An_peroxidase=PU(2.5=14.8)
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:
CACGTGCCCATCTGATCGATA
R:
CCCATGGTTCAGGGCTGTTG
Band lengths:
326-650
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]