DmeINT0036603 @ dm6
Intron Retention
Gene
FBgn0085447 | sif
Description
The gene still life is referred to in FlyBase by the symbol Dmelsif (CG34418, FBgn0085447). It is a protein_coding_gene from Dmel. It has 14 annotated transcripts and 14 polypeptides (12 unique). Gene sequence location is 3L:5657913..5749599. Its molecular function is described by: Rac guanyl-nucleotide exchange factor activity. It is involved in the biological process described with 11 unique terms, many of which group under: sensory perception of light stimulus; sensory system development; activation of GTPase activity; regulation of molecular function; sensory perception. 26 alleles are reported. The phenotypes of these alleles manifest in: retinal pigment cell; eye; mesothoracic tergum; chaeta; interommatidial bristle. The phenotypic classes of alleles include: cell number defective; behavior defective; locomotor behavior defective; phenotype. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed within 12-24 hour embryonic stages, during early larval stages, during late pupal stages, in adult male stages.
Coordinates
chr3L:5735986-5738163:+
Coord C1 exon
chr3L:5735986-5736094
Coord A exon
chr3L:5736095-5737983
Coord C2 exon
chr3L:5737984-5738163
Length
1889 bp
Sequences
Splice sites
5' ss Seq
CGAGTGAGT
5' ss Score
8.49
3' ss Seq
TCTGTCCGCCATTCAAACAGACG
3' ss Score
6.81
Exon sequences
Seq C1 exon
AATGTGCTCTTTGCGATTGGCTCGGCCTTCCTGTACTACGTCAATCACTTCAAGCTCTACTCCTCGTTCTGTGCCAGTCACAGCAAGGCGCAGAAAGTCCTGCATCCGA
Seq A exon
GTGAGTATTTCCCCCATATCATTCAGCATTACCCGCAATACCAATCCCAATCCCAATCCCCCGGACAAATCATCAAATTCATTTACATACATCAGCAGGGCGACAGTCGAGGGCGAAATATAAATGCAAAAGAAAGCAGTCACAAGATGCAGGGAAATGTTGAGAAAATTAAATTACAACTTTTATTAGCCAAATCGAAAGATGTGTATTTGCATATTACAAGATTGAAAGTGAAAGTCTCTGAAAAAAATCAAATTAACATGTATCCTTGACCAGAAGTAACAATGTTAGTGACCAGGGAATATATATTTGCATCTTTCAATTGAAACACTTGAGTATTTTTACTTTAGAGTCCGAAAGTTTTGCTTTATCAAATTTGCAAGTGCGTTACCCTCATGAAACGCACTGTACATGTGTGTTTAGCCTTTTTCGAGCACACATACCACGAACTATTGCAATCAGCGTCAAGCGTCAAAGTCTATTTGAGTTTCAGTTGAGCAAGAAACTTGTAAAAGTCAAATAACCGAAGCGAACCCATCCGAACCCACAGAGCGAACAATTGGCAAACTATTCGCTTCAATTGTGCCACGCCCCGCGCCCCACGCCCCACGCCCACACGCCCACTTTAAAATGATTTGCAAGTTAAATGAATAATTACAACCGCAAATGCCGACGACGACGGAGATGGCGACACCCCCAAAGTGGAAACCGCAAACTAAAGGCAAACTCCCGGGCCCAAAAAGGGTGTGATGTGGTGGTGGCAGCAGCATATTCATATTCATGCCAAGGCAGCCAGTAGCAGCAGCAGTGGCAACAGTGGCAGCAGCGGCAACTGTCAAGTATCTTTTGTTAATTAAACTTGTAGAATTATGACACGCTTACAAATGGCGACCCAAAACTATGCCAGGGCTCCAGAACTTCTGTCCTTTGGGTTGCGAAGAGTTGGAGGTGGTGGAACTTGGGTGCTTCACTACCACCACTACCACCACTTTCAACGCTTTCACTAAGCCCGCCTTGCAGTGAGCCGGATAAAAGGCTACTGTGGCGCGACAACATGTCATAATTAAATTAGACTTAGTCTAAGCTTAAAAACACTCGAGCAAACAGATGGCTAGATGGCCAGATGGAAGTTGGGAGCAGCCAGCAGCACATTGATTTGTGCCACGATGATGGGTTGGGATTTGCAGCTAATCAAAAGCGTTGGAGGTAAAAAAAAAATGTATTCGCAATATTTACAATCAATGAGGGAAGGTGTAGTCATGGTAACCAGGGCAGGAGGAGGGTGTAGAAGTCCTGCAAGCATCATCCACTCGAAGGGGGCGGGCGGTGGGTGATGCCACTGCGCCCGGCTGTTGCATGAAATTTTATGCAAAAAGTTGAAAGGATAATTAATTATAGCAAGAAGTGCACTTAAGTGCCTTCGTTACGTGCAAGAGCAGGAGAATCCTGTTGCGGATTGGAGGGCTGGATGGATGGCTGAATGACGGCCAGGCAGGCAGGCAGGCAGAAGGACAAGCAGCCAACGACAGACGCTATTAGACGTAAATCTGCTCCGGCTGAAGCTCCATCTCCATCCAGCTGCCTTTCCTGCTGCAGACAGGCTTTGACTTTGCCTTTATCAAAAGCTGCTCGGCTGACAATAAGAACAAGTTAATGACATTTTCTTGTCGACGTTGTGACGCTGTCATAGCCGCTGTAACTGCATATCCTTGTGCGCCATGCAACGGAACAATACCCCCCTGAATGTCTAGCATTGACTCTAATGGGCCAACGTTGCAATTAATTACACCGACTCGAACGAGCGTCCATTGAAATCGAATCATTTGGCAAATGTCTCAATTTGCATTTAAATTTTTACCCATCTCCATCTCTGTCCGCCATTCAAACAG
Seq C2 exon
ACGAGGGCAATCACGCCCTGCAGGAGTTCCTCGCAGCCAGGAATCCCAAGCAGCAGCATAGCAGCACCCTGGAATCGTATCTGATCAAGCCCATTCAGCGCATCCTCAAGTATCCACTGCTCCTGCAGCAGATGCGCAACCTCACAGACACCCGGGCCGATGAGCATGTGCATCTTTGTG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0085447:FBtr0112709:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.082
Domain overlap (PFAM):
C1:
PF0062115=RhoGEF=FE(18.9=100)
A:
NA
C2:
PF0062115=RhoGEF=FE(31.6=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0303156
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0111620, FBpp0111621, FBpp0111622, FBpp0111624, FBpp0303155, FBpp0303157, FBpp0303158, FBpp0303159, FBpp0309505, FBpp0309506, FBpp0309507, FBpp0312426
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:
ATGTGCTCTTTGCGATTGGCT
R:
CAAAGATGCACATGCTCATCGG
Band lengths:
286-2175
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)