DreINT0121673 @ danRer10
Intron Retention
Gene
ENSDARG00000004539 | ptgs2a
Description
prostaglandin-endoperoxide synthase 2a [Source:ZFIN;Acc:ZDB-GENE-020530-2]
Coordinates
chr2:21262850-21264714:-
Coord C1 exon
chr2:21264631-21264714
Coord A exon
chr2:21263097-21264630
Coord C2 exon
chr2:21262850-21263096
Length
1534 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTGT
5' ss Score
7.44
3' ss Seq
GAACATATTTTCTCCTTCAGGTT
3' ss Score
10.23
Exon sequences
Seq C1 exon
GTGGATCTGGGGCATATTTATGGAGAGACGCTGGAGGTTCAACACAAACTTCGTCTGTTTAAAGATGGAAAGCTTAAATACCAG
Seq A exon
GTTTGTGCTATAATGTGAATAATGGATATTAAACTGCACCTAAAGGGATTGTCAGGGTGCGATTTATACGTTGACGTTCGGAGGGGTCAACTTTTTCAGTAGTAGTTTGGGAATACGTGCTTCAGTGAATCAAATTTATGAATGTATTTAAATTACATCTTATTTATTAAAATGTGTACATTTTCAGTGTTTTGAGGGATATTTAGTGACTATTTTAGAGGTTACTGTCAGTTAAACTATTCAAATTATGTGTCCAATTTTTCTTTTTTTTTCTACATGCAGATATAAACACCTGCGTTACAAGAAATGTGTTTTTTGAATACTTAAGATGTCTTTCAATTGGCATGATTATGCATTTACATGGGTATAAAACATTATGGGGGCTCAAATGTATATTTATTTTCATAAATTTTTAATTATAAATATTTAAGATATAAATTAGAGATCAGCGAAAGTTATTTTTTTTACTATTAAAGGGCTGACCCCCATACATTTTGTTTTTATGTCCTTCAGGGGGATCGAGCGTTAATTAGGAGGGTCAATCCCCCCTCAAAACCCTCCCGTAATTTGTACCCCGGGGATAGTTCACTACAAAAATTGTAATTCTAACCCTCCTATTGTTTTAATTGTAATCCTCCTATTGGTTTAATTGTTTTAAACATATGTGACAAGGTTATTCAAACCCGTTCCTGGAGGTTTTAGGTCATACCTAAAATAAAATTTTACTCACTATTTACTCACTATGTTGAACACAAAGTAAGATATTTTGAAGAATGTTAGAAATTGGTCTACACTGTAAAAATTATTTGATCAATTAGTCCTGACAGCATATGTTTTTAAGTCATTGTAACTTATTAAACTAAGTTAATCATGCTCTAACTTAATTTTATAAGTTACACAAGCTGTTTTAGGTCAGTTTAGCATAATATAAGTTCAATGGACTTAAAATTTGAAGGCAACCATGATTTTTTTACAGTATATTGACTTCCATGGTAGGAAACACATATACTATAAAAGTTAATGGTAACTTGGTAATAATATTACCAGATTTTAATATTTTTCCAAATATTCTTTGTTTGTGTTCAATAAAACTAACAGATTTGTGAAAATTGAAGAGTGATGACACACTTTTCATTTTTTTGTGAACTGTCCCTTTAATTACATACACTTGAAACCACTAATTACTAGTTGGGGCTAAAATCTGTGGGCCATTGCTCCAGGAGCAGGATTACACACACCTGCTGTGTTTCTTGTTTTTCTGCTATAGAGTACAGGGGTGTCCCTGAGGGCAACTGTCCTGCAGTGTATAGCTTCAGCATGCCTCAGTCAGAACACCTGGTTGGAGGTTTATAGTATGCCTGTTAAGACCTTAGTTGACTGCTTCAGGTGTACTAAAATATGCAGGCCTACATGAGCAGGACTTGACACCCCTGATCGCCTAAAACAGAACATTTAGCCTTAAAAATGCCTTAAGTATTGCTTATTGGATCAATGTAAGACACCTAGGTAATCATGAACATATTTTCTCCTTCAG
Seq C2 exon
GTTGTGGATGGTGAGGTGTACCCTCCGCTTGTGAAGGACGTCCAGGTGGAGATGCACTACCCTCCTCATATCCCGGAAGAGCAGAAATTTGCTGTGGGCCATGAGGCCTTTGGTCTGGTTCCAGGTTTGATAATGTATGCTACCATTTGGCTCCGTGAGCACAACCGTGTCTGTGACATCATGAAGCAGGAACATCCTGACTGGGATGATGAGAGAATCTTCCAAACCACTCGTCTCATCCTGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004539:ENSDART00000006870:5
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=0.000
Domain overlap (PFAM):
C1:
PF0309810=An_peroxidase=FE(7.3=100)
A:
NA
C2:
PF0309810=An_peroxidase=FE(22.2=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:
GTGGATCTGGGGCATATTTATGGA
R:
CAGGATGAGACGAGTGGTTTGG
Band lengths:
327-1861
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]