DmeINT0016104 @ dm6
Intron Retention
Gene
FBgn0031762 | CG9098
Description
This gene is referred to in FlyBase by the symbol DmelCG9098 (FBgn0031762). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (2 unique). Gene sequence location is 2L:6007364..6012338. Its molecular function is described by: guanyl-nucleotide exchange factor activity; Ras guanyl-nucleotide exchange factor activity. It is involved in the biological process described with: small GTPase mediated signal transduction; positive regulation of peptidyl-serine phosphorylation; positive regulation of Ras protein signal transduction. 9 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: some die during pupal stage; lethal - all die before end of pupal stage. 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 06-24 hour embryonic stages, during early larval stages, at stages throughout the pupal period.
Coordinates
chr2L:6008096-6009189:-
Coord C1 exon
chr2L:6008755-6009189
Coord A exon
chr2L:6008503-6008754
Coord C2 exon
chr2L:6008096-6008502
Length
252 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAT
5' ss Score
6.6
3' ss Seq
TGTCCCACCACCTCTTTCAGATC
3' ss Score
9.16
Exon sequences
Seq C1 exon
GCAAGCAAGTTTGACTTTGAGAACTTTGTTACTTTGCTACTGCCATCTGTGGAGAACAAGCCCCTGGATGGCGATGCCCTCAACACGTTCAAGATGATGCTTCTGGAGACGGGCCCAAAGCTGCTGGCGGAGCACATCACTCGCATCGACATTGCCCTGTTTTTGGAGGAGCCGTCGAACGAGGAGGACTACTATCTGAGCTGTTCGGGTCTTGAGCTGCTAACACTGCCCCATGGAAAGGTCTTTAGGGAGGACATAATAGAGCGGACGCAGTGCATCAAGCTGATGGTCGCTGTGACCATACTCACCTGTCAAACGGATCTGGACCGAGCCCAACTGCTCAGTAAATGGATTCAGATCGCAGTGGAAACTAAGACGGCTCTCGGCAATCTGTTTGGATTCTGCGCCATCATGTTGGGCCTGTGCATGCAACAG
Seq A exon
GTGAATACTCGTTCGGTGCAGTGTACACTAAAACAAATTACTTTTTAGTTAGTTTAACGCCGAGAGGTATAAACAAGTACATTAGGTCATCACAGTTTTTTGCTTAGCAAACGAGTGATGATTTAGATGATCTTTTTATTATCACAGTTAATCACACGTGAGCAATTAGCAGTTTGGCAACTTGTTTGCAAACCATTAAGCTACATTGTTAGAGCGATACATCATAACCGATTGTCCCACCACCTCTTTCAG
Seq C2 exon
ATCCAAAAGCTCGACCAGGCCTGGCACATCCTGAGGCAACAGTACACGGACAGCGCCTTCACCTTCGAGGCCAAGTTGCGACCCACGTTGAGCATCATGAACGAGGCCTCCAATCCACAGGCTCCAAACACAACCGTTCCCCATGTTCTGCTGTATGCACTACTGATCGATCGACCCGTTATGGACATCATAAACCACTCCAACATTGACGATCGCCCAGCTCTGTACCACACCTGTATTGCTCCTTGGGAGTCGAAAGCGGATGACTTTGGCATGACCATTAATTTCCAGCACCTGGATGCATCGCGTGGCTTCCTGAAGAACTTGGAACTGTATCGAAAGAATGCCAAGATCATCCTGGAGGATGCTAGTCCTCGGCTCGATGAGCTTCTAGCTGATGCTTTTCG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0031762:FBtr0079228:7
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=0.022
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(65.9=75.9)
A:
NA
C2:
PF0061714=RasGEF=PD(32.9=40.4)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0078859
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0078860, FBpp0304851
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:
ATCAAGCTGATGGTCGCTGTG
R:
GTTGTGTTTGGAGCCTGTGGA
Band lengths:
293-545
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)