Special

DmeEX6005820 @ 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:8544544-8631123:+
Coord C1 exon
chr2L:8544544-8545233
Coord A exon
chr2L:8563739-8564296
Coord C2 exon
chr2L:8631027-8631123
Length
558 bp
Sequences
Splice sites
3' ss Seq
AACTTTCTCTCTCGTTACAGAAA
3' ss Score
10.13
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
Exon sequences
Seq C1 exon
TCTATTCATATATCCGATATAACCGTTATCGCGCCCGTGCATCTGCGTCTGCATCTGTGTGCGTGAGTCCTTGTATCCTCTGTACATATGTACAATATTTGTCGTCGTCGTCGTCGTGCATCGTTGTTGTTGTTCTTGCTGTTATCCTATTATTCATCGTCGTCCGCTGGCATTAATCTGCGTATAAAGTAAATATAACAAATTTGTGTTCTTCGGTGTTGTCTCGTGTAAGTGTCTATAATTTGTTTAAGTACGACAAGCGATCGGTGCGAATCAAAAAATTCCAATTCACCAGTCTGTGTGTGCGAATCGATAATCGAGCTATCAGAACAACCACAACAACAACAACAGCCCAATCAATCGATCAATGTCAGCAAACAAACGATAAACAGGACTCGCTGGGACTAATCAATTGCGTAATCTTCAGAATATTTTGGATTCCAACGTCTACGGAGTTTCAACTTTTGAACAATTCATTTTGCTGGACAGTTTTTGGAAAG
Seq A exon
AAATGACTGAACTTTCATCCCGCAAACCATTCGTTCGCCCATAAAACCCAGAAACAATTTAAGCCCTGTTATAAAAAAAGTTGTTGAACAAAAAATTAATCAATATATTTTGAAATAATTTAAAATCAATTTAAAGTAAAAGGTAAATGCAGCTGCAATAACTCTAAAACACGCACAACCAAGCCAAACAAACATCAAATCAAATCCATTTAGCTGCAATAAAGTTAGAGGCAAAGGCACACACAGAAAATCAACAATAATAAATGTTGCAAATTTAATCAAACCAACTGAAATTTAACTAAATTTTATGCAAAATAGAAATGTTAAATTCACACAACACAAACCACAATAACAACAGCGCCAGCAACAGCAACTACAACAAAGGCCACAAAATGCATTTGAAAAGTGCAACGGCAAAAGCAACAATAATGAAACATAAGTTAAGCAAATTTTACGGATACGGTTGGATGCAAGTCTTCCTACTACTTACAGTCCTCGTGATTGGTAATCAAAGTGCCTGGCAGGAGAATATACGACCAAAACTCTACGTTGAATTAG
Seq C2 exon
GTCCCGAAGATGTACTGAAGTTTGTGGGAAACGAAAGTGTTGTGGATCACTTCAAGCTCGTCACCAAGGATGGCAACAGTCTGCTCATCGGTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0011259-'6-9,'6-4,9-9=AN
Average complexity
A_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=0.300 C2=0.000
Domain overlap (PFAM):

C1:
NA
A:
NO
C2:
PF0140314=Sema=PU(3.6=45.5)


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)
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:
AAGTACGACAAGCGATCGGTG
R:
CGATGAGCAGACTGTTGCCAT
Band lengths:
342-900
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)