DmeINT0011344 @ 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:7939688-7940723:+
Coord C1 exon
chrX:7939688-7940424
Coord A exon
chrX:7940425-7940494
Coord C2 exon
chrX:7940495-7940723
Length
70 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGT
5' ss Score
8.54
3' ss Seq
TTCGTTTTCTGCCCTAAAAGGAA
3' ss Score
6.11
Exon sequences
Seq C1 exon
TGCGCAGCTATGACAACCACGCCAAATGCGGTCTGGTATGGGTACCGCATGTGGTGGCCTACAGGTGCCGCACTTGCGGCATATCGCCCTGCATGTCCATATGCCGGGACTGCTTCAAGAAGGGCAACCACACGAACCACGACTTCAATATGTTCCTGTCACAGGCGGGCGGTGCCTGCGATTGTGGTGACACCTCGGTCATGAAGGCGGAGGGTTTTTGCAGTGATCATGGCATCAATAATCGGGTGAATCGCGATCCGGTGCCAAACAATCTTTTGGCAGTGGCCGAGGCCATAATGCCCAAGCTGCTCTTCCGCCTGCTGCAGCACTTCCGTGAGCACAGCGACACCCCACTGGAGGTGCAAGCGATAACGTCGTACTCCTGCGAGGAGTTCGCCAACATGCTGATCGATCTGAACAACATGGGCGAAATAATGCGCAAAGTGATGACGCGCACGCTGATAAATCCGGAGGTGTATGCCTTCTTCATGGAAGCACCGTGCCAGGACACCCGGAATGGACGCTTCTTGAAGGCGAACCGAGAGAAGTACGAGGATGCCGTCAATAGATTCCCAAACCCAGAGCCACCCGATGAGTACAGAGATCTGCCCGCGCTGGGCGACAAATTGGTCCACACCACGCTACTCGAAGAGTTCATCTTCTGGACATTTAAGTTCGAGTTTCCACAGACTCTGGTCTGCTTTCTGCTGAACATGCTGCCTGATCAGGATTACAAG
Seq A exon
GTTAGTCTTGATGGGATCATATGATTTTTACATATCTATATCAATATTTATTCGTTTTCTGCCCTAAAAG
Seq C2 exon
GAACACCTCACCCGCACATTTGTGATGCACTACAGCCGCATACCGTCCGTGTTGGAAATGTCCCGTGATCCGGACACGCTCAGCAACCGGGTGGTCCACATGAGCGTCCAACTCTTCTCTAACGAAAGTCTGGCCCTCAAGATGGTCAACGAGCTGTCGCTGCTGCACGTAATGATTATTAGTCTGAAGCTAATGATGTCCAAGATACTCATACAGAATACATTGCATG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0260970:FBtr0301748:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.041 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0220715=zf-UBR=WD(100=28.9)
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:
TTTCTGCTGAACATGCTGCCT
R:
ACCATCTTGAGGGCCAGACTT
Band lengths:
182-252
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)