DmeINT0006802 @ dm6
Intron Retention
Gene
FBgn0027561 | CG18659
Description
This gene is referred to in FlyBase by the symbol DmelCG18659 (FBgn0027561). It is a protein_coding_gene from Dmel. It has 8 annotated transcripts and 8 polypeptides (6 unique). Gene sequence location is 2R:9123304..9132030. Its molecular function is described by: Rab GTPase binding; phosphatidylinositol phosphate binding; Rab guanyl-nucleotide exchange factor activity. It is involved in the biological process described with: regulation of Rab protein signal transduction; endocytic recycling; endocytosis. 8 alleles are reported. No phenotypic data is available. No phenotypic class data is available. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages, at stages throughout the pupal period.
Coordinates
chr2R:9128257-9128641:-
Coord C1 exon
chr2R:9128371-9128641
Coord A exon
chr2R:9128311-9128370
Coord C2 exon
chr2R:9128257-9128310
Length
60 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
ATCCACTTGTCCTTGAACAGCAC
3' ss Score
5.96
Exon sequences
Seq C1 exon
CACCTCGGTGCAGACATATTCCTTTGTGCACACCACTGGCGATTCGAAATGGCGCTTCGGCTTCTGTCGACAGGATCCGCGGACGAACACGGCCATGGTGCTGATAACCTACCTGCCGTGGCACGACACCTTCCTAAAGCTGCTGCCCGTGCTCGCCGAGCTGAGGCGGACGGATCCCAATGGGTTTCGCACCTTCCTCTCCGAGGCCTACAACCAGGGTATCCCGGATTGTGGCGGCAGCCTTAAAGTCTATTACAGCGCAGGCCAGAGT
Seq A exon
GTAAGTGGAGCAGCCATCAATAGTATTGGAAGAGATCTTGATCCACTTGTCCTTGAACAG
Seq C2 exon
CACTTCACCTTCGAACGCCCACTGCAGTTCCAGTTGCCCAGCATGCCAGAAAAT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0027561:FBtr0088626:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0345613=uDENN=PD(42.9=26.4),PF0214116=DENN=PU(33.9=69.2)
A:
NA
C2:
PF0214116=DENN=FE(9.1=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0087707
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0291659, FBpp0291660, FBpp0297473, FBpp0297474, FBpp0308462, FBpp0308463
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:
AATGGGTTTCGCACCTTCCTC
R:
ATTTTCTGGCATGCTGGGCAA
Band lengths:
147-207
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)