RnoINT0119676 @ rn6
Intron Retention
Gene
ENSRNOG00000015550 | Ptgds
Description
prostaglandin D2 synthase [Source:RGD Symbol;Acc:3433]
Coordinates
chr3:2688368-2689084:-
Coord C1 exon
chr3:2688912-2689084
Coord A exon
chr3:2688508-2688911
Coord C2 exon
chr3:2688368-2688507
Length
404 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CGGGCATCCACTGGTCACAGTTC
3' ss Score
2.14
Exon sequences
Seq C1 exon
TTCCTTGCTTTGCCCACGTTGCTGGCCTCAGGCTCAGACACCTGCTCTACTCCAAGCAAATGGCTGCTCTTCCAATGCTGTGGACCGGGCTGGTCCTCTTGGGTCTCTTGGGATTTCCACAGACCCCAGCCCAGGGCCATGACACAGTGCAGCCCAACTTTCAACAAGACAAG
Seq A exon
GTGAGAGGGTCCCCTACCCCACACCCGAGGAAACAGAAACCTCAGGTCAGAGCCAGGCTTTCTCTCACAAGAGAGGGTGCGTTGGGCGCTGTCAGCCATGGGAGCTGTCTGGAACCGCGCTGGCACACAGCCTGGTTGGTCCACCTGACTCCGCCAGGAATGTGGCTCTGATACCCACTTTACCGGAAGAGTAGACTGGGGCGAGCACTGGGACAAAGACGGGAGCTCAACATCCTGGGGAAGGAAGGGGTCAATGAGGCAATGAGCCAGCCTACTAGAGAGAGAGAGGGGCGTGGATGCTACCAGAACCTGTGTGTGGGAGGAGTCAGAGTAGGGAAGGCCAGCCCACTAGGGTCTGCCCATGAGGGGCGCATGGTGCAGACCCGGGCATCCACTGGTCACAG
Seq C2 exon
TTCCTGGGGCGCTGGTACAGCGCGGGCCTCGCCTCCAATTCAAGCTGGTTCCGGGAGAAGAAAGAGCTACTGTTTATGTGCCAGACAGTGGTAGCTCCCTCCACAGAAGGCGGCCTCAACCTCACCTCTACCTTCCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015550:ENSRNOT00000020926:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.079 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006118=Lipocalin=PU(31.0=95.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCCTTGCTTTGCCCACGTT
R:
AGGAAGGTAGAGGTGAGGTTGA
Band lengths:
310-714
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]