DmeINT0027605 @ dm6
Intron Retention
Gene
FBgn0010905 | Spn
Description
The gene Spinophilin is referred to in FlyBase by the symbol DmelSpn (CG16757, FBgn0010905). It is a protein_coding_gene from Dmel. It has 12 annotated transcripts and 12 polypeptides (9 unique). Gene sequence location is 3L:2505245..2554292. Its molecular function is described by: neurexin family protein binding; actin filament binding. It is involved in the biological process described with: neuron projection development; negative regulation of presynaptic active zone assembly; calcium-mediated signaling; actin filament organization. 29 alleles are reported. The phenotypes of these alleles manifest in: presynaptic active zone; embryonic/larval neuromuscular junction. The phenotypic classes of alleles include: smell perception defective; behavior defective; viable; flightless; neuroanatomy defective; partially lethal - majority die. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of low expression. Peak expression observed within 00-06 hour embryonic stages.
Coordinates
chr3L:2508639-2509500:-
Coord C1 exon
chr3L:2509364-2509500
Coord A exon
chr3L:2508866-2509363
Coord C2 exon
chr3L:2508639-2508865
Length
498 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAC
5' ss Score
5.54
3' ss Seq
ACTCTCCCCGCCCGGCACAGTGC
3' ss Score
5.24
Exon sequences
Seq C1 exon
GCGACTCGGCGATGGATCCTCGCGACATTCTAGCGACGATTACACGGAGATTAACAAGAGCCAGAGCGCCGCGGCCATCAACTGCAAGACGCTGATCAACGAGATCCGCCAGGCGGTGAACGAAGCACAGCCCAAAG
Seq A exon
GTGAACTATGACCAATCCAACCAACCAACTAGACCAGCACAATCCTCCGATTCTCTCTAGCAAGACCGTAGACTAACCCGTAGATCGAACCCAATCCCCAAGAGAGCAAAAGACGTATCATGATCATCATCTCATTTCATACAGATCTGTACATATGTTTTACTGTTCAAAAGACTTACTTAACTAATCCAACACCGTTGTTTCGTTATAACCATTTTTAATATGCGAAGGTTTTTGAGAGTTCATTGCAGCTGTTTATCCGTTTACATTACTCGCATTTCCCCATATGTATATCTCTATAAATATCTATGAATGTCTAAGCTAATCCGTTCAACCGATACCATGTGCTCTGCGTCGCAATGCCAATGGATCCAGTGCGATCTTACTAACTCTGACTTTTCTATCTCTCCGCTTCTTTCTCTCTCGACTAACCCATAACCCGCAATCGTTCCAAAGTTAAACAAGTCGTTCCACAATCACTCTCCCCGCCCGGCACAG
Seq C2 exon
TGCCCTGGCAGCAGCAGCACCACCAGCAAATCCAGCAGCAGCCGTCCGCCCACACCACCGGTCCGCCGTCGCCCACCAGCATGTCCTCGGGCTGCTCCTCGCCCGGATACTCCCCCAGCCGCACCCTGGACCTGTCCGGTTCCAGCTCTAGTTTCTCCGATCGCAAGGCGATGGCAGCGGGGTATACCTACAAGGGTGGCCCTGTTCATGAATGGACCAAGGATCAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0010905:FBtr0304613:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.744 A=NA C2=0.803
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053625=SAM_1=PU(9.5=7.9)
Main Inclusion Isoform:
FBpp0311290
Main Skipping Isoform:
FBpp0293157
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0293155, FBpp0293156, FBpp0293159, FBpp0293160, FBpp0293161, FBpp0293162, FBpp0311289
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:
CGATGGATCCTCGCGACATTC
R:
GGTCCATTCATGAACAGGGCC
Band lengths:
346-844
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)