DmeINT0005833 @ dm6
Intron Retention
Gene
FBgn0037698 | CG16779
Description
This gene is referred to in FlyBase by the symbol DmelCG16779 (FBgn0037698). It is a protein_coding_gene from Dmel. It has 6 annotated transcripts and 6 polypeptides (4 unique). Gene sequence location is 3R:9461084..9493677. Its molecular function is described by: transcription regulatory region sequence-specific DNA binding; transcription factor binding; DNA-binding transcription factor activity. The biological processes in which it is involved are not known. 10 alleles are reported. The phenotype of these alleles manifest in: wing. The phenotypic classes of alleles include: visible; viable; lethal. 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 12-24 hour embryonic stages, during early larval stages, during late pupal stages, in adult male stages.
Coordinates
chr3R:9474717-9475840:-
Coord C1 exon
chr3R:9475534-9475840
Coord A exon
chr3R:9475382-9475533
Coord C2 exon
chr3R:9474717-9475381
Length
152 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TTGCCCTTGGCTCCTTACAGCTC
3' ss Score
8.78
Exon sequences
Seq C1 exon
GTACCAAAGAGCATCCATCTGCCATTGACGACTCTCAGCAGCGCGCCGCGCGTGTTGATGTGCAGCGCATCCGTGGGCACCGAAGGATCCGTCACTCTGCAATTGCGTGATGCGAACGCGTTGGAGGCAGCAGCAACAAAGACAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCGGCAGCCACATCGACGACGTCACCAAATGGCGTTGCAGGTGCGCCAGCGTCGACGCTAGAGAATGCGCTGACCATCGGGTATCCGGATCCGGAAATGTTGGCAGATGTCTTGGGCACCATTCAGACAGCCT
Seq A exon
GTAAGTGAATTATATACAAACATGTGTGCAAGGTAGTTCTAGCTTCTTATCAGTATCTGAACTCGTTTGAAGAAGTACTTGTAGAATTGCATAATGTGCCCATCTACATTATATTTCCATGATTCTTACCTATTGCCCTTGGCTCCTTACAG
Seq C2 exon
CTCTCAAGAACAACAACTCAATCACAGCAGCAACTTCAAGCAATAGCTCGACCAAGTCGACGAGCAGCAATCATCTGACAAATCCCAACAAGATAACCATAAAAAGGCGGAGTGTGCACTCAGTGAGCACCTCGACGAACAGCAGTAGCATTAGTAGTTGCAGCAGCAGCAGCAGCAGTAGCAACAGTGGCAAGAGCAATACCAGCTACATCAAGAACTGCTTGATACGCAGCAGCAGCTGCAGCAACACGGTCACCAATGTCACCACATTGGCCCAGATTATGAGCAACAGCAGCACGAGCAGCGCGGCCAGTTTACTCAATCAGCACAACAACAACAGCAACTGCAGCAATAGCAGCAACTTCAGTACCGCCTCCTCGGTGGGCAGCAGCATCAGCGTTGGCAGCAACAGCAGCAGCAGCAACTGCAGCAACGGCAGCAACAGCAACAGCAACGACAGCAACAGCAGCAGCGGCGGCGGTCACCGATTGAGTTTCAAGGGCACCGGACGGCATGTTCCCGCGAGCGGATTAAGTTCATCGGCGGCATCCACGAACACGAACGGTACCGTCAGCGGCATTGGCGGCATCATAAGCGTCGAGGCGCCCCGCAAGAATCGACCCAAATTATCATCGCCAACGCGTCACGGACCGCAGCAGTGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0037698:FBtr0082125:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.345 A=NA C2=0.559
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0081603
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0303767, FBpp0303768, FBpp0303769, FBpp0311930
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:
CACTCTGCAATTGCGTGATGC
R:
TGCTTGAAGTTGCTGCTGTGA
Band lengths:
257-409
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)