DreINT0121676 @ danRer10
Intron Retention
Gene
ENSDARG00000004539 | ptgs2a
Description
prostaglandin-endoperoxide synthase 2a [Source:ZFIN;Acc:ZDB-GENE-020530-2]
Coordinates
chr2:21258435-21261256:-
Coord C1 exon
chr2:21261109-21261256
Coord A exon
chr2:21259109-21261108
Coord C2 exon
chr2:21258435-21259108
Length
2000 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTTTCTCTTTGGTAAAACAGGAG
3' ss Score
5.21
Exon sequences
Seq C1 exon
GTGTCTGGTGGACGTAACCTGCCACCTGCAGTTCAAGGAGTCGCTGTTAAAGTTCTGGAACAAACCAGACAGATGCGCTATCAATCTTTCAATGCATACAGAAGACGCTTCAACATGAAGCCCTACTCATCCTTTGAGGAGATGACAG
Seq A exon
GTAAGACTGGTGTCAATCCCACAGGCCCTAAATATAGGACTTAGCCATTCTAGTTAGCTGAAGTGAAATACAATACACACTAAAATAATAAAAATATTTTTATTTTTAAGATTTACTTTTGGCCTCTATTAAGTGGATAGGACAGTATTTCAGATAGGAACAAAGTGGGAGAGAGAAAGGGGGTAGAGAGGGGAAATGCCCTTAAGCCAGGATTCAAACTTGGGATACCCTTAAGTGCCACTGCACCATGTGTCAGTGCGCTAACCATTAGGCTATTGCGCCAACAAATAATAACAATATTGACACACAAGAGCAAAATCCATGAAATCCTTTTAAAATTTTAAATGATAAAAAATAACCAATGGCGACACGGTAGCTCAGTGGTAAACACTGTCACCTTACAGCAAGAAGGTCACTGGTTTGAATCTCGGATGCTCCAGTTGGCATTTCTGTATGGAGTTTGCATGTTCTCCGCATGTTTGCATGGGTTTTCTCTGGGTGCTTCGGCTTCCCCCACAGTCCTAAGACGCTATGTGAATTGAGTAAGCTAAATTGGTTGTAGTGTATGTATGTGAATGTGAGAGTGGAAGGGCATCCGCTGAGGAAAACATATCCTGGAATAGTTGGAGATTAATTCTGCTTTGGCAACCTCTGATAAATCAGAGACTAAGCTGAAGGAAGATTAATGAACGAATGAAACGACAACCAATCAGAATCCTCCTTATCATTTAAACTGGTGAACGACATACTTGTGAGCATGTTTATAACAAACAGACTGTTGTTAAAGGGATAGTTCACCCAAAACTGACATTTCTGCCATCATTTACTCACCCTTCACTTGACAATCCCATTTGAGTTTTTCTTCTGTTGAACACAAAAGAAGCTATTTTGTAACCATTAAATCAGTAATCATTGACTTCCATAGTATTTGTTTTTCCAACTATGGATGTAAATAGTTTTCAACTTTCTTCAAAGCATCTTCTTTATTGTTCGACAGAAGAAACTATTATTGTTTCCTGCACTGTTAAACATGCTGGGTTCTACACAATTAATCTGTGTTGGGACAACATGAAGAAATTAGTTAGCTTATTAAATTTTACAGGTTATACACTGTAAAAAAATGCAAGGTTCCACACAATTCATTCATGTTGTCTCACTACAAATTGATTAAGTTAACGTAACACTTTTAACAAACTTATGTGGATTGAACATAAAAAAATTAAGCTGCCCCAATGAAATCTCAAGAATTGGGTTGTTTCAGCTCAGCTTTTAAATAAGTAGTTTGAACAAGCAAAAAAATATATATATTTTTGAGTGTAAGATAAGTTACAGATTTAAGTGGATTGAACAATGGGGTATATGAACGGTTAATGGGACTTTTTTTGTTTTATACGATTCCTTTTATAGCATCTATGTTGTTGTAATGTAATTAAAATATAATCAGTAAATATACTTTAGCATTCATTTAGTTTCTCAAACGTAAACACAATGAAAAGTCGTTTTCACGCATGTTCCCATCAGGATTAGCAGGCTAGCGCAGTCGCTACATTGAATATACTGGGGTAAAATAAATGTTCATATTTTAAACTTTTATTTAAAGCTTTTTGAACATTATGAGACACTCTTTGAATCGGATATCACTTAGCCAGTGGAGATCACTGATTTTAAAAGAAAACAGACTTAAACGCGACAGTTTTGTTACGGCATACAGTTCACCGGAAGCGGCTGACCAAGGTTACTAAAAAATTTAAAGTACTTCTGCATACTGCTGCATATCCCCTATACAATTAAGTTGTCGCATAAATAAGCCCCTCAGAAATATATTGTTTTAGCTAATTTTAAATGAGTAGTTCAAACAGCAAACGTCATTTTTGAGTGTAGTGTGAATGGGCTTTAACTGTATAATAAGGAACTTCAAAAATGATACTTGCACAGATTTAGAAGTGACACATTATGTAACCTCTTGTTTAATTAAAATGGTTTTCTCTTTGGTAAAACAG
Seq C2 exon
GAGACAAAGATCTGGCTGCCCAGCTGAAGGAGCTGTACGGTCACGTAGACAAGGTTGAGCTGTATCCTGGCCTTCTTGTGGAGAAATCCAGACCCAACTCTGTGTTTGGGGAGACTATGGTGGAAATGGGAGCTCCCTACTCTCTCAAAGGCCTCATGGGAAATGCTATTTGTTCTCCTGAATACTGGAAGCCCAGCACATTTGGTGGGAAAGTGGGATTTGACATCGTTAACTCGGCTTCACTGAAGAAATTGGTGTGTTTGAACGTCAGTGGGCCCTGTCCGATGGTGTCCTTTCAGGTGCCAGATGTGAAATTTCAGAGTTCAGAAAACGTGAATTCAAGTTCAGTGCACTCCACAGTAAATAATATAAATCCAACTGTTGTTTTGAACGAGCGGAGTTCAGAGCTGTAAAAGGTCTCAAAATCTTCAAAATCCCAGATACTTGATATGGTTTTGTAATTTATTTATTTTTTATATATATTTATTTGAATAATTTATTGCAGTAGTGTATTTATTGATTGTTTTTTTTTTTTGTATTGTGATCGATGTGCAACTTTGTTTCATAAATTCATGTGAGGTATTCAACTAATTGGACAAACACATTTCAAATGCCAATCAACTGTTGCAAATGTTTATTTCATAAATAAAAACAAATGATATTTTGCAAAAATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004539:ENSDART00000006870:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.015
Domain overlap (PFAM):
C1:
PF0309810=An_peroxidase=FE(13.3=100)
A:
NA
C2:
PF0309810=An_peroxidase=PD(27.1=72.5)
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:
CCACCTGCAGTTCAAGGAGTC
R:
CCACTTTCCCACCAAATGTGC
Band lengths:
343-2343
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]