Special

DmeEX6005811 @ dm6

Exon Skipping

Gene
FBgn0011259 | Sema-1a
Description
The gene Semaphorin 1a is referred to in FlyBase by the symbol DmelSema1a (CG18405, FBgn0011259). It is a protein_coding_gene from Dmel. It has 8 annotated transcripts and 8 polypeptides (6 unique). Gene sequence location is 2L:8542147..8672041. Its molecular function is described by: protein binding; chemorepellent activity; heparin binding; semaphorin receptor binding. It is involved in the biological process described with 13 unique terms, many of which group under: negative chemotaxis; negative regulation of cellular component movement; stem cell differentiation; positive regulation of cellular component movement; cell recognition. 57 alleles are reported. The phenotypes of these alleles manifest in: cellular anatomical entity; non-connected developing system; transverse nerve; adult head segment; motor neuron. The phenotypic classes of alleles include: viable; increased mortality during development; phenotype; increased mortality. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of very low expression. Peak expression observed within 12-18 embryonic stages.
Coordinates
chr2L:8660648-8661487:+
Coord C1 exon
chr2L:8660648-8660759
Coord A exon
chr2L:8661146-8661288
Coord C2 exon
chr2L:8661359-8661487
Length
143 bp
Sequences
Splice sites
3' ss Seq
AATTTTACGTCTGTTCGCAGCGA
3' ss Score
7.59
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
Exon sequences
Seq C1 exon
ATCAACCCAAAGATGGCAGCTACGACGATGGTAAATTAATCATTGTGACGGACAGTCAGGTGGTAGCCATACAATTGCATCGTTGTCACAATGACAAAATCACCAGCTGCAG
Seq A exon
CGAGTGCGTCGCATTGCAGGATCCGTACTGCGCCTGGGACAAAATCGCTGGCAAGTGCCGTTCCCACGGCGCTCCCCGATGGCTAGAGGAGAACTATTTCTACCAGAATGTGGCCACTGGCCAGCATGCGGCCTGCCCCTCAG
Seq C2 exon
GCAAAATCAATTCAAAGGATGCCAACGCTGGGGAGCAGAAGGGCTTCCGCAACGACATGGACTTATTGGATTCGCGACGCCAGAGCAAGGATCAGGAAATAATCGACAATATTGATAAGAACTTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0011259-'21-23,'21-22,22-23=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact

ORF disruption upon sequence exclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.000 A=0.000 C2=0.320
Domain overlap (PFAM):

C1:
PF0143720=PSI=PU(15.6=26.3)
A:
PF0143720=PSI=FE(75.0=100)
C2:
PF0143720=PSI=PD(7.8=11.4)


Main Inclusion Isoform:
FBpp0302962


Main Skipping Isoform:
NA


Other Inclusion Isoforms:
FBpp0079302, FBpp0292880, FBpp0292881, FBpp0292882, FBpp0302963, FBpp0302964


Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
ALTERNATIVE
Chicken
(galGal4)
ALTERNATIVE
Chicken
(galGal3)
ALTERNATIVE
Chicken
(galGal3)
ALTERNATIVE
Zebrafish
(danRer10)
ALTERNATIVE
Zebrafish
(danRer10)
ALTERNATIVE
Zebrafish
(danRer10)
Primers PCR
Suggestions for RT-PCR validation
F:
AACCCAAAGATGGCAGCTACG
R:
TTGTCGATTATTTCCTGATCCTTGCT
Band lengths:
218-361
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)