Special

DmeINT0034803 @ 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:9900761-9902965:+
Coord C1 exon
chr3L:9900761-9901018
Coord A exon
chr3L:9901019-9902150
Coord C2 exon
chr3L:9902151-9902965
Length
1132 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGA
5' ss Score
5.73
3' ss Seq
GTTTTGTGTTTTTTTTTTAGGCG
3' ss Score
10.56
Exon sequences
Seq C1 exon
ATCTCAAACAAGAGCTGAACGTCAAGTCACGCTTTACCCCAGTGGTCAATGGAACGAGCGTTCCCACGGCAAACGACACAAATACGGTCAACAGCTCGATGAACTCGTCCGCCTCGCTGCCAAATGGTATTGTTGCCAATGGCGAATTGGTAAAACACGACAATGCTGTCGCCACAAGAGCCACCAGCGTCAGCGTCAACGCCCTCAATGGCAGTTTAGTTAATAGAAACGAATATAACCAGCAGCATTCGCTTAAGA
Seq A exon
GTAAGATACTAAGTTCCCTAAAGAAAACCAGACGCGCGCTAAAACTGTCCAAGACGAATCGCCAAACGTTCAAGCCATGCATTTAGTATTGTTTTTCCATTTGTTTCTTTTTTACTTGTTAACCAAAAAATGTAGCCCGCTTAAGTTCCTCATAATTTGTAATTGTATTGTAAATTATTAAAATTAAGAGCCCAAATGTGACGAAAGAGTTTGCAACATTTCTTGTAGGCGATTTTTGTACGATTTGTGTTTGCGTCTGTAGCTAGTAGTTGACCTAACTAACCTCTCGACTAACATGCTGTGTACGTGTGCTTCCTCTTGCAGATCCCGAGAATCAAATCAATGGCAATTCCATGAACCCCAGCTCCCGCACAACGGCGCTCAACATTGTGGCCGACATGTTAAGAAAACTAAACGTAAGTCCCTCCGCAAACTATAAGTCCAGCATGCCATCCTACCTCATCCATTGTTTCGTATGTACATATGATCCTTGAACCCTTCACTCCCACCATCGGCTTATGTGTTTTTCCCTATGTTTTTAGTGGGACAAGGCACTGCTATGTCCCGAGTGCGAAAAGTTTCGCTGCATGTGTGAGCGCCCGGCAAGTGTGCAGCCGCCGCCGCCGCCATCGGCCAGCGAGGCAAGTCTTTTTCGCCGCGCCTTTGGCGGCAGCAGCAGCTCAGTGGCCACCAGTAGCGCCCAGTCCACGCCCACCAGCGATTGCAGCTCCGCCGGAAGCCTCAGTGCGGGCTCAAACATTTTTAGGCGCTTCGCCGAGCGCATGCGAAACTCGCCGGACGCCAGCCTGCCGCTCTGACAATGCGCTCGGAACTTTAAGGCTAATTTTAGTTGCCCTCCGCTTGCATTTATTAATTGCATTGGTTAATAAATACAAAATTTATTTGTACCTTATTTTATGTTCTTTGTTTTTGTTCGTTATGATTTATTCAGTTTCGAAAGCGCATAATAACTTGGCTTGCTGACTAAACTCTGCACTGGGCAAACCGTTGCGAAATGAAATTTTCATTAATTTATTTATTATATGATGTGCCCAAATCCTTCTATAGTTAATTTTTCATATAGTTCACTGACTGTTGCTTAATCCGCTCTCGTTTTGTGTTTTTTTTTTAG
Seq C2 exon
GCGATGGAGACGAAACTGAAGACGTACCGCGAGAATGGTCAGCCAATGCCGCAGCGACACCGCTCCTCCCAGCAATCCACACATCCGGCGCTGGCCGGACTGCCTTGCTTCTCGCTGGATGCCGAGTAGTGTGGATTCTGCAGTTCAGCGTGATCCACAAACCCCAAATCCGAAACCCAATCACCTAGGGCGGGATACTGTTCAGTTGGCTTTACGTTTACGTTACGTTACTTTAATGTTACTGTTCGCATTAATTAAGTTTCTGCTGCCTCTTTATTTATTTGAACTAAAATGACTTTGTATAAACCACTTGCGATATTATGAATTACACAACAGTTGATGTTGTTGTTTCGAGCCCAACATATATAACATGCCTTAGTACGAATTAAGTGTATACCTAAGCTATAAGTACCCACTCGGTTCACTTTTGACTTGAATTGTTAACTCGAACGCAATTGTTTTGGCATACAATGTGTTTAGCGACTAAGTTCAAAGTTGATCAACCAGCAAAACAAGCGAAGAAGCTCTGTCCAAGTATTATACTTCAAGCGGACAACCAATACTCGTAGCGTTTAGGAAAAAGACAAGATCTAACCCGGGAAAAAAAATTATTAAAATTATCGAAACGATCATCTAGTTATATTGTAACTATCCCCAGAGCTATTTTCTGTTTATATTTACCAGCGAATATAAATTTGTAAAAATGCAAAATATTGCTAACGGCAAACTGTATAAAGCATAACAAAACTCCAACGAACAGGCAAACAAAATATATATATATATGTATGAATAAAGAGCAAAATAATTAGTTTAAT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0036059:FBtr0076344:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact

Alternative protein isoforms

No structure available
Features
Disorder rate (Iupred):
  C1=0.804 A=NA C2=0.608
Domain overlap (PFAM):

C1:
PF048808=NUDE_C=PD(70.4=87.0)
A:
NA
C2:
PF048808=NUDE_C=PD(0.8=1.6)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0076073


Other Inclusion Isoforms:
FBpp0112071, FBpp0113092, FBpp0311743, FBpp0311744


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:
GTGGTCAATGGAACGAGCGTT
R:
ATCCACACTACTCGGCATCCA
Band lengths:
353-1485
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)