Special

DmeEX0006403 @ dm6

Exon Skipping

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:17677826-17683499:-
Coord C1 exon
chr2R:17683393-17683499
Coord A exon
chr2R:17678272-17678782
Coord C2 exon
chr2R:17677826-17677919
Length
511 bp
Sequences
Splice sites
3' ss Seq
ATTGTTTTTTTCAATTGCAGGTT
3' ss Score
11.01
5' ss Seq
CAAGTATGT
5' ss Score
7.44
Exon sequences
Seq C1 exon
GGTCACTTTTAAAATGGCCGTCGATCAGTGAAGTTGTATACACTTTTTTCGTGTTCCGTGTTTTTCGCTTAATTTGATCGTTTATTTAAATGTTTTTATGAATTTTG
Seq A exon
GTTTTGCGTTTTCCCTTTTGCCACCAACAGCTAATTGCATTAAAATAAAACCAACAAGTTGTTCTGCTGGGCGTAAATCATTGTGTCGTTGTCGCTGACACTCGAATACTTATAGCCAGATGCTGAAGCAGCAGCAGCAGCAGCAGCAGCAGCGACAATAACACCAGTAATCAGCACAACTATCGACGACAATGGCAGACATCGGACATCAGAATGCGAGGCGTCAGTGATTAAAAGCAGTCGGAGAGGCCAGCCAGCCATCCAACCAGCCAGCCAGGCAGCCCCATTGGCACCACGAGCAAAAAGCAGCTGAATCATCAGAACTCGGAGGAGTAGTGGAGTACTAGTTTCGCGCATCTCCTACTACAAGCCAGCAGAATGAGCTCCAAGAGCAGACCTTCATCGGCGGCGATGTTAGTTAATGCGATACCCATGATACTGCTGATCACCTTATCCGGCCTGACGATCGTGGCAGGTTGGATGCCCGACGTGAAGCCTGATTTGCAAACAA
Seq C2 exon
AACAAGACAAAGTCCTAGCCCATTTTATAGGCAACTCGACGGACTATTTCAAGATTTTGGACCACAACGATGAGTTTGTTCTAGTTGGTGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0016059-'0-4,'0-3,12-4
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (Ref, Alt. ATG (>10 exons))

No structure available
Features
Disorder rate (Iupred):
  C1=NA A=0.044 C2=0.000
Domain overlap (PFAM):

C1:
NA
A:
NO
C2:
PF0140314=Sema=PU(3.5=46.9)


Main Inclusion Isoform:
FBpp0086050


Main Skipping Isoform:
NA


Other Inclusion Isoforms:
FBpp0089289, FBpp0291371


Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
Chicken
(galGal4)
Chicken
(galGal4)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
HIGH PSI
Zebrafish
(danRer10)
HIGH PSI
Zebrafish
(danRer10)
HIGH PSI
Zebrafish
(danRer10)
Zebrafish
(danRer10)
HIGH PSI
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCACTTTTAAAATGGCCGTCG
R:
TGGCACCAACTAGAACAAACTCA
Band lengths:
200-711
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)