DmeINT0027191 @ dm6
Intron Retention
Gene
FBgn0016059 | Sema-1b
Description
The gene Semaphorin 1b is referred to in FlyBase by the symbol DmelSema1b (CG6446, FBgn0016059). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (1 unique). Gene sequence location is 2R:17672839..17683499. Its molecular function is described by: chemorepellent activity; semaphorin receptor binding. It is involved in the biological process described with 7 unique terms, many of which group under: positive regulation of biological process; mesenchymal cell differentiation; regulation of cell size; negative chemotaxis; regulation of biological process. 16 alleles are reported. The phenotypes of these alleles manifest in: intersegmental nerve; filamentous actin. The phenotypic classes of alleles include: locomotor behavior defective; neuroanatomy defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-18 hour embryonic stages, during early pupal stages.
Coordinates
chr2R:17677826-17678782:-
Coord C1 exon
chr2R:17678272-17678782
Coord A exon
chr2R:17677920-17678271
Coord C2 exon
chr2R:17677826-17677919
Length
352 bp
Sequences
Splice sites
5' ss Seq
CAAGTATGT
5' ss Score
7.44
3' ss Seq
GCTTCTTTCTTTCTTTGCAGAAC
3' ss Score
12.39
Exon sequences
Seq C1 exon
GTTTTGCGTTTTCCCTTTTGCCACCAACAGCTAATTGCATTAAAATAAAACCAACAAGTTGTTCTGCTGGGCGTAAATCATTGTGTCGTTGTCGCTGACACTCGAATACTTATAGCCAGATGCTGAAGCAGCAGCAGCAGCAGCAGCAGCAGCGACAATAACACCAGTAATCAGCACAACTATCGACGACAATGGCAGACATCGGACATCAGAATGCGAGGCGTCAGTGATTAAAAGCAGTCGGAGAGGCCAGCCAGCCATCCAACCAGCCAGCCAGGCAGCCCCATTGGCACCACGAGCAAAAAGCAGCTGAATCATCAGAACTCGGAGGAGTAGTGGAGTACTAGTTTCGCGCATCTCCTACTACAAGCCAGCAGAATGAGCTCCAAGAGCAGACCTTCATCGGCGGCGATGTTAGTTAATGCGATACCCATGATACTGCTGATCACCTTATCCGGCCTGACGATCGTGGCAGGTTGGATGCCCGACGTGAAGCCTGATTTGCAAACAA
Seq A exon
GTATGTGGCAGTAGTTGGAATCCTTATTCTTCAATCTAACTTTATAACTATTTGTTTATTTGTGTCATTTGTTTGGGTTTTTGCTTTCCGGTCTTGTTGCTGCTGGTTTATCAATGACAAAAGCGAGGCTGTTCAAGCTAAGCTCCGATTTTCCAAGCTGCTTATCAGGCGGAATTTTCGCAATGCCAGCAGCAACAAGCGCTAGCATTTCCTCTGAATCGAGTTAAACAGAAATTAAAATGAAATTGTGCAAGATCTCAAAAAAAAAAAAAAAAAAAACACGAGTAAACGCACAAGTTATATAATCCCAGCAGTCAATAACATTTCACTTTGCTTCTTTCTTTCTTTGCAG
Seq C2 exon
AACAAGACAAAGTCCTAGCCCATTTTATAGGCAACTCGACGGACTATTTCAAGATTTTGGACCACAACGATGAGTTTGTTCTAGTTGGTGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0016059:FBtr0086890:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.044 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(3.5=46.9)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0086050
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0089289, FBpp0291371
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:
GAATGCGAGGCGTCAGTGATT
R:
TGAAATAGTCCGTCGAGTTGCC
Band lengths:
351-703
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)