DmeINT0034059 @ dm6
Intron Retention
Gene
FBgn0016038 | mod(r)
Description
The gene Vacuolar protein sorting 37A is referred to in FlyBase by the symbol DmelVsp37A (CG17828, FBgn0016038). It is a protein_coding_gene from Dmel. It has 7 annotated transcripts and 7 polypeptides (2 unique). Gene sequence location is X:621530..623051. Its molecular function is described by: . It is involved in the biological process described with: endosome transport via multivesicular body sorting pathway; ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway; protein targeting to vacuole; protein targeting to membrane. 8 alleles are reported. The phenotype of these alleles manifest in: wing. The phenotypic class of alleles includes: viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed within 00-12 hour embryonic stages, during late larval stages, at stages throughout the pupal period, in stages of adults of both sexes.
Coordinates
chrX:622207-623051:+
Coord C1 exon
chrX:622207-622358
Coord A exon
chrX:622359-622433
Coord C2 exon
chrX:622434-623051
Length
75 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GCATTCCATTTCCCCTGAAGGAG
3' ss Score
5.46
Exon sequences
Seq C1 exon
GAGAGAACGAGTGCAAGGGCATTCATCTGGTAGAGCTGAAGCGCCGACTCAGCGACGATTTTACAGCTTTAAAAAACCTAGGCGAGAAATGCGACCGGCTGAACAAGAAGTACTTCAAGAAGTCGGATGAATACGCGCCTCAGCATATCAGG
Seq A exon
GTGAGTTCCCTTAAAAAGCCAATGGCGTGGGAGTTACCATTCCCATCCGTAACTTGCATTCCATTTCCCCTGAAG
Seq C2 exon
GAGCTTCTTCAGATTGCAGCTTCCAATGCCGATGGCGACTGCGATCGTCACGTGGAGCACTTCCTGAACGGAAAGACCGACGTGCAGACTTTCCTCAACACGTACCAGTGGTCGAAGAAGATCAGTACCGAGCGCAAGGCCAAAGAGGAGCGCCTGGGCACCCAGCTCAGTGCTCTGGAGCGGGCCGGTATCTAGGATTGCCGTGACACTCCCTGGCCGTGCCATCCAGAGCACGGTCCTCCCACTCCTCGCACTCCTCCCACACCGCCACGATCCGCGTCGCAATAGTAGAGAATATCAATGTTAGTAAATAGAGAAGTTAAGCCAGAGATGGGGCGACATAATCATGGCACACACGGCCACGCATTCCCAGAACAGAAAGCAAAACCTTGTTGAAGTAATAAGAAGGTGCACTAGTTGTTCGTTTCCCAAGATCGTTTACTTGGGAAGAGGGTCTTGTTATTCTATCCGTACCCCGAAACGAAGCACTATGTGCAACAGAACGCAGTCCGGAATCGCATGTATTACCTATTTACTTTTTTTCCTTTTGGTTAATCGTGAGCCCCATCCATATATTCTCTCCATATATACATATATATTAAAAAAAAACTATGCTTT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0016038:FBtr0089726:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.010 A=NA C2=0.048
Domain overlap (PFAM):
C1:
PF072008=Mod_r=FE(34.2=100)
A:
NA
C2:
PF072008=Mod_r=PD(34.0=78.5)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0088666
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0088664, FBpp0088665, FBpp0088667, FBpp0307122, FBpp0307123
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:
GCCGACTCAGCGACGATTTTA
R:
GAAGTGCTCCACGTGACGATC
Band lengths:
173-248
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)