DmeINT0003647 @ dm6
Intron Retention
Gene
FBgn0035677 | CG13293
Description
This gene is referred to in FlyBase by the symbol DmelCG13293 (FBgn0035677). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (3 unique). Gene sequence location is 3L:6082883..6092188. Its molecular function is described by: transcription corepressor activity. It is involved in the biological process described with: transcription, DNA-templated. 8 alleles are reported. No phenotypic data is available. The phenotypic class of alleles includes: viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed within 06-24 hour embryonic stages, during early larval stages, at stages throughout the pupal period.
Coordinates
chr3L:6087668-6088077:+
Coord C1 exon
chr3L:6087668-6087898
Coord A exon
chr3L:6087899-6087954
Coord C2 exon
chr3L:6087955-6088077
Length
56 bp
Sequences
Splice sites
5' ss Seq
CACGTAATT
5' ss Score
4.34
3' ss Seq
ATCCCCAGATTTCCCCGCAGCTA
3' ss Score
5.27
Exon sequences
Seq C1 exon
CTTAAGAACCAGCGAAACCAACTACCTGAACGAGGCGTATCAGTTCTATGCGGCAATTAGGGGTCGAGCCTACTATTCGCGGGCAGCCAAGGAGGATCGACCGGATCTGATGGTGAAAAAGCTGCGTTACTATGCCCGTTTCATTGTGGTGTGCCTGCTGCTCAAGAAGATGAAGCTGGTGCGGGAACTGGTCACCGAGTTGGAAAAACAAATACAGGAGTACACCAACAC
Seq A exon
GTAATTACTTGGTGACCCATTTTTGACTCCGTATTAATCCCCAGATTTCCCCGCAG
Seq C2 exon
CTACGAGCCGGAGGATCATTTGGAGTGGTCGCTGGTGCTCGAGGAGATCAAGGGCTTCATCAAGGCGGAGGCGGCGGTGGCCGTACTGCACGCCGACTCCAATCCCATCATCCTGTCGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0035677:FBtr0332061:4
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:
PF120703=DUF3550=FE(14.4=100)
A:
NA
C2:
PF120703=DUF3550=FE(7.7=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0304371
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0304372, FBpp0304374
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:
GTGCCTGCTGCTCAAGAAGAT
R:
CGCCTTGATGAAGCCCTTGAT
Band lengths:
148-204
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)