DmeINT0014188 @ dm6
Intron Retention
Gene
FBgn0038296 | CG6752
Description
This gene is referred to in FlyBase by the symbol DmelCG6752 (FBgn0038296). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (1 unique). Gene sequence location is 3R:15191058..15196210. Its molecular function is described by: ubiquitin protein ligase activity; ubiquitin-protein transferase activity; zinc ion binding. It is involved in the biological process described with: proteolysis involved in cellular protein catabolic process. 8 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: viable; fertile. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed at stages throughout the pupal period, in adult male stages.
Coordinates
chr3R:15195267-15195804:-
Coord C1 exon
chr3R:15195558-15195804
Coord A exon
chr3R:15195413-15195557
Coord C2 exon
chr3R:15195267-15195412
Length
145 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATC
5' ss Score
7.05
3' ss Seq
AACGTGTCATTTATATACAGATC
3' ss Score
6.8
Exon sequences
Seq C1 exon
GCAGATGCTCATAGTGCGAACCTGGCTAGATGACAAGTTCCAACAAATCCAGACCGACAGCAATGAAGAGATTCGGCGCCTGTACATGGAGACAGAGAGCCGCATTGGCCCGGATCTTACCATATTCGATGTGGACTATACGACTACAGTGCGGGTATCCTCGGATCGCCTAGCCCTGCGCTCCCAGGGCAGCTTCAACACGGTCCGGGCTAATTGTTGCGTGTACGGCGGTCGCTGGATGTATGAG
Seq A exon
GTAATCGCTATTACATGGAGTGGGAGGAGTAGCTAAAGATTGGGGAATGAGTGGTAGATTCGACGGTGGTTGACCACCGGTCATTGACTCGTATTGAGGAGTGTGGGTTGCTCGTGCGTACTAAGAACGTGTCATTTATATACAG
Seq C2 exon
ATCCACCTCCACACTAAGGGCGTAATGCAGATTGGTTGGGCCTCCAACTCCTGCCAGTTTAACGAAAACAGCGGGGTGGGAGATACCAAGTCCAGCTATGGATACGATGGCAGCAAACAGCAGATCTGGCATATATCCACCAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0038296:FBtr0083029:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0062223=SPRY=PU(4.9=7.2)
A:
NA
C2:
PF0062223=SPRY=FE(39.3=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0082488
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0297356
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:
GTGCGAACCTGGCTAGATGAC
R:
TACGCCCTTAGTGTGGAGGTG
Band lengths:
258-403
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)