DmeINT0019546 @ dm6
Intron Retention
Gene
FBgn0261046 | Dscam3
Description
The gene Down syndrome cell adhesion molecule 3 is referred to in FlyBase by the symbol DmelDscam3 (CG31190, FBgn0261046). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (4 unique). Gene sequence location is 3R:17473935..17505667. Its molecular function is described by: identical protein binding; cell-cell adhesion mediator activity. It is involved in the biological process described with: homophilic cell adhesion via plasma membrane adhesion molecules; axon guidance; dendrite self-avoidance. 17 alleles are reported. The phenotype of these alleles manifest in: commissure. The phenotypic classes of alleles include: viable; neuroanatomy defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of no expression detected. Peak expression observed during early larval stages, at stages throughout the pupal period.
Coordinates
chr3R:17490286-17491847:-
Coord C1 exon
chr3R:17491727-17491847
Coord A exon
chr3R:17490404-17491726
Coord C2 exon
chr3R:17490286-17490403
Length
1323 bp
Sequences
Splice sites
5' ss Seq
TACGTGAGT
5' ss Score
7.77
3' ss Seq
ATACTCACTCTGATTTATAGCTG
3' ss Score
5.3
Exon sequences
Seq C1 exon
AGTTAAGCAAGAATCTGGCTCCTCGGACCACCCAGAAACCGGTGATGGAGATTCACGTGGAGCGTGGAAACGACGTTCATCTGCCGTGCAACATCCAGGGCAACCCATTTCCCATATTTAC
Seq A exon
GTGAGTCAACCAATTGCCAAGCCAAAAAGGCCTGGCTTGCTATCTGTGGAATGGGTGTATCTGTATCCAAGTATCTACGCAGCTGGCAATAAAATAACATCACGAGGTTCCGGTTTGGAGATTATAGACAGCCCTTAAGTGCATTTGAATGTTTGCCTGGGGATGCTGTTTTTATTGCATATTAGGGACTGATGTTTTAGTGCTAATTAGGTGACTTCATGGATGAAACGAGGCCATGTGCTAATAGCAGGGAGGAAAACAAACTAATAAAGGCACAGACTGGAAAGCCAATCCGCACACTAACTTGGTATTGAAGTAACTTGATCATCTTGTTTGCCCACTCACAATGGATTGACTTACTGGACCCAACACTTTGTTGGCCGAACATTAAAAAGCAATTCGGGTCCACGAAAGTTGGGCCAATAACACATATCAAGTAACCACTGACTTCAACCCTCCTCACAGATAATTAGCAAAATAAAACAGTTTGCAAGGACCTCAATAGGGTAGCATAACTTAACAGTCTGTTTCACTTAGCAGGGCTTATTAAAATTTCACGCAGTTCTAAACACTAGATGAGCCCCTCACGAATATGTGGAAGTACATACATACATTTTCGCGACAAGGACGCAGACAGCTCGAAAAATCAAAATACACAAGACAAACATGTACAGAGCAAAGTTCTCGCTGGGAAAACATAAATGCCGAGCCAGACGGGAAAAGTGCCTGAAAGGAGGAGGAAATTCCCAACTGATTACTATAATCGCAGAAGAAGGGCGATAATTTTGTTTTGGGCATAAGTTCAGGCGTGGCTGGAATAACAAACTAGGTTCCTTGGTTTTATTGATTTCGTGTGTGATTCTGTAACTGATTGAGTTTCCAGTTTCTCTCCGTAGTAGTACATTTCACTTAGTGAGCTTAAAAGAGTTTGGTTTTCTTTCTAGGTTTTCAGAAATTTATTTAACTTTTAGATTGGTATTGCTTTTGAAACTGGAACGCTATTAAATATGTTTTTAGAACACTGCATTCGACTAATTGAATCAAATTGTTTATTACTTTCAATTGAAAAACTGTTAGTATTTGTCCAAATAATGTTTGTTTTCTTAAAATACCTGAGGGAAGCATTGAAGTGCAGTGCTTCTGTGCAAATAAAATTAAGTTTATTGATCTGAGCTAGTCAGCATGTGAGACAGATACTGTTTGCAGATACAGCTCGACGAGCAGCAGGCCCGAATTTAAATCAATAAAGAGCTTGTGCCTTCGGCAAAGGCTTTGCCAACCAGCTTTACATATACTCGTATATATACTCACTCTGATTTATAG
Seq C2 exon
CTGGTATCGCGTTTCCGACTCGGCAGCCCTCTATCCCATACCCTCGTCACAGCGAGTGATACTTTCGCGCACACTGCTGCTCATCAAAAATGCTGACGAACGCGATGCGGGCAAGTGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0261046:FBtr0113397:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.073 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(35.9=80.5)
A:
NA
C2:
PF0767911=I-set=FE(42.4=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0303244
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0112309, FBpp0112310, FBpp0303245
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:
AAGCAAGAATCTGGCTCCTCG
R:
TCGCGTTCGTCAGCATTTTTG
Band lengths:
222-1545
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)