DmeINT0020468 @ dm6
Intron Retention
Gene
FBgn0035916 | GAPsec
Description
The gene GTPase activating protein, SECIS-dependent read-through is referred to in FlyBase by the symbol DmelGAPsec (CG5978, FBgn0035916). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 3L:8622039..8623901. Its molecular function is described by: GTPase activator activity; translation elongation factor binding; Rab GTPase binding; GTPase binding. It is involved in the biological process described with: activation of GTPase activity; regulation of GTPase activity; intracellular protein transport; translational readthrough. 6 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 within 00-18 hour embryonic stages, during late larval stages, at stages throughout the pupal period.
Coordinates
chr3L:8622411-8623549:-
Coord C1 exon
chr3L:8623077-8623549
Coord A exon
chr3L:8622935-8623076
Coord C2 exon
chr3L:8622411-8622934
Length
142 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
AATATGTGTGCTCTATATAGATA
3' ss Score
6.61
Exon sequences
Seq C1 exon
GTGTGCCCGATGTGCAGAGTTTTCGAGCACTCAGTTGGAAGCTACTCCTTGGCTATTTGGGGCCTAGGCGCAGTAGTTGGACCACAACCTTGGCCCAAAAGCGAGCCCTGTATAAACAGTTCATCGAGGAGCTAGTCCTGCCCCCCGGACACTCGAGCAATAGAGCTAGCGTAGACGGAGGAGATGGGGACAAAGTCGATTCGGGGGGCGTTGGCCTGCAAGATCATCCGCTGAGCGAGGGACCCGAAAGCGCGTGGAACACGTTCTTCAATGATAACGAGTTTCTACTGCAAATCGACAAGGATGTCCGCCGCTTGTGCCCGGACATATCCTTTTTCCAGCAGCCCACCGATTATCCCTGCGAGATTGTGGTCCACAGCAAAGGAGAGCATGGACGAAGGCTCCACGAACGGGTGGTTCCCGCCGTTCTAAGTTCGGCGAATGTGGAACGCAAGGGCCTCGGCATGACAAAG
Seq A exon
GTGAGTTCAAGATCGGAATTGTGCTAGACAATAAGCTCAGAATGTGTTGTTTCATTCATGCATACCGTGTGGATTTTAGCAGCAAGTAAGTAAGCCCATCTGGAACTGCCCCAAACCTAATGAATATGTGTGCTCTATATAG
Seq C2 exon
ATAAATTTGATTACAAAACGCTCCGTTGAAAACTATGCCGCCATGGAGGAGGGCCAAGAGGCTCACTGGGAAGTTGTGCAACGCATTTTGTTCATCTATGCCAAACTAAATCCCGGCCAGGGATATGTCCAGGGCATGAACGAAATCGTGGGACCCATTTACTATGTTATGGCCTCCGATCCTGACCTCACATATCGCGCCCACGCTGAGGCTGATTGTTTCTTTTGTTTTACCGCCCTGATGAGCGAGATAAGAGACTTTTTTATTAAAACACTAGACGACGCAGAAGGCGGCATCAAGTTCATGATGGCCAGGCTATCGAATATGCTGAAATCAAAGGACCTAAGCATTTACGAGCTACTCAGGAGCCAAGAGCTGCATCCGCAGTATTACAGCTTCAGGTGGCTCACACTGCTCCTGTCGCAGGAGTTTCCACTGCCAGATGTACTGCGCATTTGGGATTCCGTGTTTGCGGACGAACAGCGATTTGATTTTCTGATAAAAATATGCTGTTCAATGATATT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0035916:FBtr0076648:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.171 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0056613=RabGAP-TBC=PU(4.2=5.1)
A:
NA
C2:
PF0056613=RabGAP-TBC=FE(91.1=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0076372
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
GCAAAGGAGAGCATGGACGAA
R:
CGATTTCGTTCATGCCCTGGA
Band lengths:
243-385
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)