DmeINT0036698 @ dm6
Intron Retention
Gene
FBgn0264089 | sli
Description
The gene slit is referred to in FlyBase by the symbol Dmelsli (CG43758, FBgn0264089). It is a protein_coding_gene from Dmel. It has 7 annotated transcripts and 7 polypeptides (4 unique). Gene sequence location is 2R:15869495..15922118. Its molecular function is described by: Roundabout binding; heparin binding; calcium ion binding. It is involved in the biological process described with 21 unique terms, many of which group under: embryo development; positive regulation of cell motility; positive regulation of cell adhesion; positive regulation of response to external stimulus; exocrine system development. 79 alleles are reported. The phenotypes of these alleles manifest in: plasma membrane bounded cell projection; segmental subdivision of organ system; cell projection; larval multidendritic neuron; neuron projection. The phenotypic classes of alleles include: lethal - all die before end of prepupal stage; phenotype; cell shape defective; increased mortality during development.
Coordinates
chr2R:15877031-15877540:-
Coord C1 exon
chr2R:15877172-15877540
Coord A exon
chr2R:15877103-15877171
Coord C2 exon
chr2R:15877031-15877102
Length
69 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
ACTTGGCATTCCATTCGCAGCGA
3' ss Score
7.88
Exon sequences
Seq C1 exon
GAACCTCGCATCGAATCCATTCAATTGCAATTGTCATTTGGCCTGGTTCGCGGAATGGCTGCGCAAAAAATCACTGAACGGCGGAGCGGCACGTTGTGGAGCCCCGTCGAAGGTACGTGACGTGCAGATCAAGGACTTGCCCCACTCGGAATTCAAGTGTAGCAGCGAGAACAGCGAGGGCTGCCTGGGCGATGGCTACTGTCCGCCATCCTGCACCTGCACCGGCACCGTGGTCCGCTGTTCGCGTAACCAGCTGAAGGAGATACCGCGCGGCATTCCCGCCGAGACATCGGAGCTGTATCTGGAGTCCAATGAGATCGAGCAGATTCACTACGAACGCATACGCCATTTGCGCTCCCTTACCCGACT
Seq A exon
GTAAGTATCTATCTACATTGTGCATCCCAAAGACGTTTGCTAATTCGCCACTTGGCATTCCATTCGCAG
Seq C2 exon
CGATCTCAGCAACAACCAGATCACCATTCTCTCCAACTACACCTTTGCCAATCTGACCAAGCTGTCCACGCT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0264089:FBtr0330729:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF138551=LRR_8=PD(11.5=5.6),PF0146213=LRRNT=WD(100=22.6),PF127992=LRR_4=PU(62.5=20.2)
A:
NA
C2:
PF127992=LRR_4=PD(35.0=56.0),PF138551=LRR_8=PU(8.2=20.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0303578
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0303573, FBpp0303574, FBpp0303575, FBpp0303576, FBpp0303577
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:
ACCAGCTGAAGGAGATACCGC
R:
TGGTCAGATTGGCAAAGGTGT
Band lengths:
180-249
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)