DreINT0121675 @ danRer10
Intron Retention
Gene
ENSDARG00000004539 | ptgs2a
Description
prostaglandin-endoperoxide synthase 2a [Source:ZFIN;Acc:ZDB-GENE-020530-2]
Coordinates
chr2:21261109-21262035:-
Coord C1 exon
chr2:21261749-21262035
Coord A exon
chr2:21261257-21261748
Coord C2 exon
chr2:21261109-21261256
Length
492 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
AAATTTTTGTGTGTGAACAGGTG
3' ss Score
8.38
Exon sequences
Seq C1 exon
GTGAGACCATCAAAATTGTGATCGAGGACTATGTTCAGCACTTGAGTGGATACAACTTCAAGCTCAAGTTTGACCCAGAGCTCATCTTCAGTGAGCGTTTCCAGTACCAGAACCGTATTGCGGCCGAATTCAATACCCTGTATCACTGGCATCCACTGTTGCCGGACAACTTTCAGATCCAGGATCAGATCTACGGCTATCACCAGTTTGTGTTTAACAACTCTATCGTCACCACACATGGCATTCGCAACATGGTGGACTCCTTCACCAAACAGACTGCTGGACGG
Seq A exon
GTGAGTTTCATTCAGGGTTTAGACCAGTTCACTCCACACCAAAAGTACATTCAGCAGATCAGAGTACAACATAAGCACAGATTAAACATGATAATAGTGAAAATAAGCTCAATCAGATGGCAATAAAGTTTGCACATTGATGCACAAAAACTTGATGAAGCATCTGCTGCTATAAGTTGTAACATTGTGAATTGTCCTATAGTTTTTAAGAGACTCCTAATACAACTTCAGTCTAATGTAACTTCTGTGGAACACAAAAGGAGATCTGTTTTTTGTCCATACAATGAAAGTCAGGGAGGTTCAGCATTGCCAACTGGCTTTTGCAATATCCCTTGTGTTCCAAAAAATTTAAACAAATAAAAATTGAGAAAGTCATACAGGTTTAGAACAACATGGATGTGTTTGTAAATGATGAGTAAATGTGAATTATTGGGTGAACGTTCACTTATGTTCTTTGTTTGCTGATTTTTACAAATTTTTGTGTGTGAACAG
Seq C2 exon
GTGTCTGGTGGACGTAACCTGCCACCTGCAGTTCAAGGAGTCGCTGTTAAAGTTCTGGAACAAACCAGACAGATGCGCTATCAATCTTTCAATGCATACAGAAGACGCTTCAACATGAAGCCCTACTCATCCTTTGAGGAGATGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004539:ENSDART00000006870:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0309810=An_peroxidase=FE(25.7=100)
A:
NA
C2:
PF0309810=An_peroxidase=FE(13.3=100)
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:
TCGAGGACTATGTTCAGCACT
R:
AGCGCATCTGTCTGGTTTGTT
Band lengths:
345-837
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]