DmeINT0034799 @ dm6
Intron Retention
Gene
FBgn0036059 | nudE
Description
The gene nudE is referred to in FlyBase by the symbol Dmel
udE (CG8104, FBgn0036059). It is a protein_coding_gene from Dmel. It has 6 annotated transcripts and 6 polypeptides (4 unique). Gene sequence location is 3L:9899241..9903031. Its molecular function is described by: microtubule binding. It is involved in the biological process described with 20 unique terms, many of which group under: organelle fission; anatomical structure formation involved in morphogenesis; regulation of microtubule motor activity; spindle localization; regulation of nervous system development. 19 alleles are reported. The phenotypes of these alleles manifest in: cellular anatomical entity; microtubule cytoskeleton; neuron projection; intracellular organelle; cell projection. The phenotypic classes of alleles include: lethal; viable; neuroanatomy defective; mitotic cell cycle defective; visible; body color defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed at stages throughout embryogenesis, during late larval stages, at stages throughout the pupal period, in stages of adults of both sexes.
Coordinates
chr3L:9899241-9900084:+
Coord C1 exon
chr3L:9899241-9899355
Coord A exon
chr3L:9899356-9899725
Coord C2 exon
chr3L:9899726-9900084
Length
370 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
TTTTCTTCGCCGACTTCTAGTCT
3' ss Score
6.14
Exon sequences
Seq C1 exon
AGCCAGGGTTGGCTTGTGCGTTTTTGGAGTAGTGGTAAATTTTTACGAGCATAACTATTTACACTGATTTTATGTAAATAAAACAAACAAAACGTAGCAAAATTAAGTGCAAAGT
Seq A exon
GTAAGTAGTAAATGTGGACAGTCGTGCTGTATAAAATTCTAGGTATAAACACTGGAATTCTACGAAAAAATCACCGATGATTTCATTTCCATGCAGTGCGTTGTTGTATGGGAAACTTCGTCGTAGCTATTTGTTGTTGTTGTTGTTGCTGCTGCTCATCACCATCATCCTCGTTGTTTTCGTTGTTGTTGCCGCAGCAGCTGCGTCACAAAAATGAGTTTTGTTTAATTTGATTTTATTTACATTTGATATGGACAAAACCGACTGCCCTTTTAGGGCATCGAACAAGAACAACAGCAACAGTAACTACAAAATTCAGGGCAAACACCTGTTCCTAATTGATTTTTCACTTTTCTTCGCCGACTTCTAG
Seq C2 exon
TCTATTCACCACCCCCAACACACAAAACAAAAAAAAAGTAAAACTACGACTTGAACAACAACTGTGTTTTGGCATTTTAATCACAGCAATTAAAAACAAAGCAGCCAAAAAACACGAATAAATAACCCAAACAGTAATAGACCAACCGTAGTACATAGCATTGTTCAGAAATTAAAAGTTAAATCAATTCGAACGAACGAAATTACAAACCCATTTTGACCGCCGATTAGTACACAAAAACCAGAAAAAGGAGTTAGCAGCTAAGGAAAATTTGCAGAAATGGAGTCGCCCCCGATGTTCAATAGTGTGGAAGATGAGTGCAGATATTGGAAGGAACGATCTAAGCAGTACCACAAAGA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0036059:FBtr0076344:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.222
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0076073, FBpp0112071, FBpp0112072, FBpp0113092, FBpp0311743, FBpp0311744
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:
GTTGGCTTGTGCGTTTTTGGA
R:
TGTGTACTAATCGGCGGTCAA
Band lengths:
344-714
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)