DmeINT0009419 @ dm6
Intron Retention
Gene
FBgn0053276 | CG33276
Description
The gene Ubiquitin-related modifier 1 is referred to in FlyBase by the symbol DmelUrm1 (CG33276, FBgn0053276). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 3L:7639811..7640446. Its molecular function is described by: protein tag; sulfur carrier activity. It is involved in the biological process described with: negative regulation of JNK cascade; tRNA wobble position uridine thiolation; protein urmylation. 14 alleles are reported. The phenotype of these alleles manifest in: anterior crossvein. The phenotypic classes of alleles include: increased mortality during development; phenotype; increased mortality; visible. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of very low expression. Peak expression observed within 00-18 hour embryonic stages, at stages throughout the larval period, during early pupal stages, in adult female stages.
Coordinates
chr3L:7640125-7640337:-
Coord C1 exon
chr3L:7640270-7640337
Coord A exon
chr3L:7640207-7640269
Coord C2 exon
chr3L:7640125-7640206
Length
63 bp
Sequences
Splice sites
5' ss Seq
AATGTATGT
5' ss Score
5.87
3' ss Seq
GAATTATATATATTTTAAAGGGA
3' ss Score
4.78
Exon sequences
Seq C1 exon
TGCAGGGGCGGAGTTACTATTTGGTAACATAAAACGCCGTGAATTGAACTTGGACGGTAAACAAAAAT
Seq A exon
GTATGTTCTAAAAGATGTTTTAAACTTGAGTGAAATCGGTTATGAATTATATATATTTTAAAG
Seq C2 exon
GGACTATTGCTAATCTGCTTAAGTGGATGCATGCGAATATTTTAACGGAGCGTCCGGAACTTTTTCTTCAAGGAGATACTGT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0053276:FBtr0114530:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF091386=Urm1=FE(24.2=100)
A:
NA
C2:
PF091386=Urm1=FE(28.4=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0113022
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:
TGCAGGGGCGGAGTTACTATT
R:
AGAAAAAGTTCCGGACGCTCC
Band lengths:
135-198
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)