Special

DmeINT0011346 @ dm6

Intron Retention

Gene
FBgn0260970 | CG42593
Description
The gene Ubr3 ubiquitin ligase is referred to in FlyBase by the symbol DmelUbr3 (CG42593, FBgn0260970). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (3 unique). Gene sequence location is X:7935896..7953883. Its molecular function is described by: ubiquitin protein ligase activity; protein binding; zinc ion binding. It is involved in the biological process described with 6 unique terms, many of which group under: regulation of cellular process; positive regulation of biological process; regulation of cell death; cellular protein modification process; cell death. 26 alleles are reported. The phenotypes of these alleles manifest in: visual system; eye-antennal disc; cell; antennal segment; sensillum. The phenotypic classes of alleles include: lethal - all die before end of pupal stage; phenotype; lethal - all die before end of prepupal stage; increased mortality during development. 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 00-06 hour embryonic stages.
Coordinates
chrX:7940783-7941414:+
Coord C1 exon
chrX:7940783-7941195
Coord A exon
chrX:7941196-7941255
Coord C2 exon
chrX:7941256-7941414
Length
60 bp
Sequences
Splice sites
5' ss Seq
ATGGTTGGT
5' ss Score
5.29
3' ss Seq
CCTTTTATTTATCCGTGCAGGAG
3' ss Score
9.07
Exon sequences
Seq C1 exon
ATCCCAACAAGAATTTTCATTTCGTCATCGACTGCACGCGTCAGGTGATGAAGGACCACTGCTACTGGCCACTAGTCTCGGACTTTAACAACGTCCTTTCACACGAATCGGTGGCCCTGGTCTTTCTGCGGGACGACAATCTCATCGATATGTGGTTCCAGTTTCTCCAGATGCTCCAGGGCATGAATGTCAATGTGCGCGAGACGGCTTCTCATGTGGAATTCGAGCCAAATAGCTACTATGCGGCGTTCTCCTGTGAGCTTGAGGCCAGTGCCTATCCCATGTGGTCGATTATCTCGCATCTGCAGGATGGCACACATGCCCATCTGGCAAAGAAGATCATCAACTACTGTGTGACGACGCTGCACGAGTGGCTAGACTCTATTTACTTTATGGAGGCGCGTCTATCTATG
Seq A exon
GTTGGTATTTTCAATCCGTTTATTGCAGTTTCAATAAAATCCTTTTATTTATCCGTGCAG
Seq C2 exon
GAGGAGATGATGCAGGCTTCGTTCCACTTTCCCCTGCATCGTTATCTGGCTGCCTTTGTTTGCCAGGCGGTAACTAAAATGGGAATCAGTCTGAACGATGTGCTGCCCTCACGCCCCTATCTGCTGCCCCTGCTGATGATCCATCCACTTCGCGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0260970:FBtr0301748:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact

Alternative protein isoforms

No structure available
Features
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):

C1:
NO
A:
NA
C2:
NO


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0303730


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0290962, FBpp0303731
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:
AACTACTGTGTGACGACGCTG
R:
AGTTACCGCCTGGCAAACAAA
Band lengths:
144-204
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)