DmeINT0013878 @ dm6
Intron Retention
Gene
FBgn0039464 | CG6330
Description
This gene is referred to in FlyBase by the symbol DmelCG6330 (FBgn0039464). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3R:26949692..26958491. Its molecular function is described by: uridine phosphorylase activity. It is involved in the biological process described with: nucleoside metabolic process; gravitaxis; nucleotide catabolic process. 24 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: female fertile; fertile; gravitaxis defective; viable; lethal. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 06-24 hour embryonic stages, during early larval stages, during early pupal stages.
Coordinates
chr3R:26951775-26953254:-
Coord C1 exon
chr3R:26953004-26953254
Coord A exon
chr3R:26951899-26953003
Coord C2 exon
chr3R:26951775-26951898
Length
1105 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGG
5' ss Score
9.63
3' ss Seq
TGCATTCGCTTTAATTGCAGGTA
3' ss Score
8.38
Exon sequences
Seq C1 exon
ATTTTTTCAGTCTCGCTCGAAGCGTTGACGTGTCTACACGAGTAACTAGTTTTGTTTTGGCTCGCTGGCTGCTCCTTCGTCTGGTAGTTGGTAGTTCGTTTGTGAGTTAAAGGACATTCGAGAGGTGACATCATGCCGCCCACCATAACCGATAATCAGACGCACGACTTTAAGGCCCACTACGATTGCGCCCACAGGTCCTCGCTGCAGGACGACGAGACGGACGATGCGTACGTGAAAAGGATAACGCG
Seq A exon
GTAAGGATGCTGAAACCGGTTTTTGGTCCTGCAGCTGCTTCTTAAGTCAGCCGGGGGTTGTTTCATTTGGCGCGAGAAAGTTGCTCTGGAAATTTCTCTGTTTGCTAGCAACAAATAACAGCCGTTTTCTATTGAAAAATGAAAACAAATGCAAATCAAAATCCATCTGCAATGCAGTCTATAGTTTGCCTGATGTCAAATCGCTGTGTTGGCACAAAACCAGCTCTTCATCTGAGCAAAGAACGCCAATGGAAAACAGAACGCTTGGCCAGTTGGCACAATATTTGCACAGACCGGTGGGTGTGACGCCTACTCGATTACCCTGTATTCATTTCAAAGATCACTTTTCATCCTATCCGATTTCCGAGCTCATCAAATCATAATTTATGCTTCAATCGGATGTTTGCCGGAGTGCTTACGAAATATATTCACTTCGCGCTTATCAATCAAGGTCAAGACTACACGGGGTTTTCATTTGATTATGCTAGAGTCATAGACATTTTGCTTTTTGTTTTGCTCACACTTCTAACATGTTTTTTTTCCGACTCCCCGTTTGACGCACTTGATAATGATATTGGTTGGGTATTGGTGCTCTCTAGACCCCCTACATCGCAAGGGGGGTCTCTATAAATAAAGTCACTAATACACGAATCAATTCTGATCCAAATATTGATTAGAAATACGAAATTTGAATCTGTCATTTTGTGGCCATTAAATACTCGAATAGTGCTTACTCACGATTGTGTGACAAAATTGTGTGTATAAGTAATGTATATTTCATAAAAATTAGCTCATAACAATGTGTTTTTGCTAAGCATTACCTAAAAAATAAATAATTATTCCAGCGATGACGAATTTCTTCCTGCCCATCCCAACTGATTACACTTTTGGGGGGCTTGTTCGGCCACCGATTTTCTAGGAAACACTTAGATAAACTTATCTTTTATCAGAAAACGAGCATTTTTAAGTGTGATTTACTTCTGACAGCTGAAAGTAATTAACTCATTCATTTCTTGGCCTGAAGTGGGCGTTTATTTATGGCCCCCGCTGGCGGCGAATAGAATTTAATCCTCATTAATTCGTTTTGCATTCGCTTTAATTGCAG
Seq C2 exon
GTACTCCGATGGAACCGTCAAATTGCGCAACTCGAACATTGAGCTCATGGACCAGGATATCCTCTATCACCTGGCCTTGGGCAGCGAGAGCCACGACCTGCAGGAGATGTTTGGCGACGTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0039464:FBtr0085085:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.175 A=NA C2=0.012
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0104815=PNP_UDP_1=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0084457
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
CGAAGCGTTGACGTGTCTACA
R:
AACGTCGCCAAACATCTCCTG
Band lengths:
355-1460
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)