DmeINT0027170 @ dm6
Intron Retention
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:8543330-8545233:+
Coord C1 exon
chr2L:8543330-8543715
Coord A exon
chr2L:8543716-8544543
Coord C2 exon
chr2L:8544544-8545233
Length
828 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
TCCTTCTCCCATTTCCACAGTAT
3' ss Score
8.9
Exon sequences
Seq C1 exon
TGCCATTTGAGACTGAACTCTCTTTCGTGCGAGTTCCCTTTTCATTCGAAAATTTAACGCCCGCGCTGCTGCAGCGCGTTGTTGCTCCGGTTGGAAAATATCTGAAAACAGCATTAATAAATAAACAAAAATATTGGATAAATCGCCGGTAGAAACGCTGCATAAAACGAAATTTGGTTTCTTGTAAAATATTATTTTTCAAGATATTTTCTTGTTAATTTCCGGATATTCGACAAGGATATAAATGTTTCTTTCGCGTTGATAAACAAATTCCAGCACCGCTACCTTTGTGTCGCGCAATTGTGAAAAGTGATTTGTCCATTGTGTACATTAATTAATAAATTGGTAATTGCTCAATTTAGAAACATGTGCAATCGAGAGCTAGT
Seq A exon
GTGAGTGTTTGTGTGCAACAATAATAAAGCCGAAAATTGCCCAATTGCAATTGGCAATCACAACAAAATTGGAATATTATGGCACATTAGAAAAAGAAAATAACGAAAACTGTGTTTCCACCCAAAGTTTAGGCCGCAGCAGAGCGAATCCACAAAAATATACAATTTCGGCAATTTTTCCACATATTTTTCATTGATTTTTCGCCATCCTGCGGGTGTGAGCAAGAGGGCGAGAGAGTTGAAAGGAGAGCCAGGCTTTTGTATTCTGTTTTGGGTACGTTTTGGGAATGAAACGGTCCTGGCTCTCGCTAACCCACCCTCCCTCTCTCTTTGGGATTATCCTTTTTATATTTTGTTTATTTCTCTATTTTCCTGGCCACGTTTTGTGCACCATTCGTTTCGCTGCATTTCATTCTCGCGGCGTTTCAAATTGACTCAGAGAGAGTGAGAGTAAGAGTGGGAGAGAGCAGCACTCTCTTATTCTTCTTCCTCAAACTCACGCACCCCCCGCATAATGTTTTTCGACTCTGCCTTGTGCCCCCCATTCGCATCTCTCCGCAGCGCGTTGCCAACCAAAAAAAGAAAACTAAAGTACTGTTGTCATAATAAGAAATTTATCAGGAAAAAAGTTGAATTACAAAGTGTTTCAATTGATATTTCTTGATCATTTCTTCATCAAATCGTGTTTCATATCGTAGCAAATATTAATTTTAATTCAAAAAGCCCTACATGCCAGATATTTGTGTTCAAGATAAGCTCTTCCTGCGGCCATAACTTTTGATTGGGAAACTGAAATCTAATCCAGTTTTCCTTCTCCCATTTCCACAG
Seq C2 exon
TATTTAAGCCAGAAACAAAGTGAATAAGGCAAATTTGAATAAAGAAAAAGAATAAACCAAGAAAATATGCTCAGAAATCGCATCCGTAGCCTACTTATCGCATGAAGAACCGGTACCGTTAAGGGATAATCGCCGTCGCGTTAATTCGACTCCTGCACCGCACCGCCCCGCCCCCCCGTTCGTCGTTTCGTCTATTCATATATCCGATATAACCGTTATCGCGCCCGTGCATCTGCGTCTGCATCTGTGTGCGTGAGTCCTTGTATCCTCTGTACATATGTACAATATTTGTCGTCGTCGTCGTCGTGCATCGTTGTTGTTGTTCTTGCTGTTATCCTATTATTCATCGTCGTCCGCTGGCATTAATCTGCGTATAAAGTAAATATAACAAATTTGTGTTCTTCGGTGTTGTCTCGTGTAAGTGTCTATAATTTGTTTAAGTACGACAAGCGATCGGTGCGAATCAAAAAATTCCAATTCACCAGTCTGTGTGTGCGAATCGATAATCGAGCTATCAGAACAACCACAACAACAACAACAGCCCAATCAATCGATCAATGTCAGCAAACAAACGATAAACAGGACTCGCTGGGACTAATCAATTGCGTAATCTTCAGAATATTTTGGATTCCAACGTCTACGGAGTTTCAACTTTTGAACAATTCATTTTGCTGGACAGTTTTTGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0011259:FBtr0079691:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
ATTCCAGCACCGCTACCTTTG
R:
CGGGCGCGATAACGGTTATAT
Band lengths:
344-1172
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)