DmeINT0024876 @ dm6
Intron Retention
Gene
FBgn0038237 | Pde6
Description
The gene Phosphodiesterase 6 is referred to in FlyBase by the symbol DmelPde6 (CG8279, FBgn0038237). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (2 unique). Gene sequence location is 3R:14513901..14558304. Its molecular function is described by: protein binding; 3',5'-cyclic-GMP phosphodiesterase activity. It is involved in the biological process described with: cGMP metabolic process; signal transduction; negative regulation of nucleobase-containing compound transport. 15 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: fertile; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed within 12-24 hour embryonic stages, during early larval stages, during late pupal stages, in adult male stages.
Coordinates
chr3R:14516310-14516759:-
Coord C1 exon
chr3R:14516606-14516759
Coord A exon
chr3R:14516470-14516605
Coord C2 exon
chr3R:14516310-14516469
Length
136 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
CTTATTTCAATTGATCTTAGTGC
3' ss Score
5
Exon sequences
Seq C1 exon
GCCTTGTCACCTGAGGACTATCGTTCAGTCATGAAGACCGTGGAAAGCGCCATTCTGTCCACCGATCTGGCCATGTATTTCAAGAAAAGGAACGCTTTCCTAGAGTTGGTGGAAAATGGGGAATTCGATTGGCAGGGCGAGGAGAAGAAAGATT
Seq A exon
GTGAGTCCAAATAAATGCTGATCCCAGTGTTAACAATTTTTTACCCATTTTTGAAGTTTGGCTTAGCTTTAAGATTTATTCTTGTATTTCTTATAATTAAACCCTTAACAAAATACCTTATTTCAATTGATCTTAG
Seq C2 exon
TGCTTTGTGGCATGATGATGACTGCTTGCGATGTGAGTGCCATTGCCAAGCCCTGGGAGGTTCAGCACAAGGTTGCCAAGTTGGTGGCCGATGAGTTCTTTGACCAAGGAGATCTCGAAAAGCTGCAGCTTAACACCCAACCAGTCGCCATGATGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0038237:FBtr0300330:12
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=0.037
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(21.3=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(22.2=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0303081
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0289559, FBpp0311378
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCACCGATCTGGCCATGTAT
R:
ACTGGTTGGGTGTTAAGCTGC
Band lengths:
242-378
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Neural diversity
- Neurogenesis
- Neuronal activity
- Splicing factor regulation (brain)
- Splicing factor regulation (SL2)