DmeINT0010600 @ dm6
Intron Retention
Gene
FBgn0034800 | CG3788
Description
This gene is referred to in FlyBase by the symbol DmelCG3788 (FBgn0034800). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (1 unique). Gene sequence location is 2R:22932035..22934077. Its molecular function is described by: uridine phosphorylase activity. It is involved in the biological process described with: nucleotide catabolic process; nucleoside metabolic process. 5 alleles are reported. No phenotypic data is available. The phenotypic class of alleles includes: viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of very low expression. Peak expression observed in adult male stages.
Coordinates
chr2R:22933119-22933523:-
Coord C1 exon
chr2R:22933384-22933523
Coord A exon
chr2R:22933319-22933383
Coord C2 exon
chr2R:22933119-22933318
Length
65 bp
Sequences
Splice sites
5' ss Seq
AGGGTGACT
5' ss Score
2.76
3' ss Seq
ACACAGACCGCATCCCATAGCCA
3' ss Score
0.98
Exon sequences
Seq C1 exon
TCAAACTTTAAATAGACACTCATTCCGGAAGTAAGACAAAATTGCTGGAAGTAACTTAAAAATTAAAAAAACAAAAATGTCCAAAAGCAACTGCAGTGACTGCACATGCCGTTTGGCCAACGAGGTGGGCCAGCTAAAGG
Seq A exon
GTGACTACTTTCAGTTTAGACAGGAGTTTCCTGAGATCCCTCATAACACAGACCGCATCCCATAG
Seq C2 exon
CCATCGTGAATGCCCAGAGCAGGACGCTCGCCAAGCTGGTCCGTCAGATGAAGGAAGGCTGCAAAAAGGACGAGGAGGCCAAGGAATCCACATTGTGCGGCCTGAATCCCTGCCTGAAGTGCCTGCAGCCTGACATACTCTACCACCTGGGCCTGAATACGGAGACCACGGACTTTCCCAAGGTTTTTGGTGATGTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0034800:FBtr0071995:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0104815=PNP_UDP_1=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0071904
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0292517
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:
TCCAAAAGCAACTGCAGTGACT
R:
GCACTTCAGGCAGGGATTCAG
Band lengths:
183-248
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)