DmeALTA0002794-2/2 @ dm6
Alternative 3'ss
Gene
FBgn0259244 | CG42342
Description
This gene is referred to in FlyBase by the symbol DmelCG42342 (FBgn0259244). It is a protein_coding_gene from Dmel. It has 13 annotated transcripts and 13 polypeptides (12 unique). Gene sequence location is 3R:16502770..16571363. Its molecular function is described by: extracellular matrix structural constituent. It is involved in the biological process described with: extracellular matrix organization. 29 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: fertile; viable; lethal. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of very low expression. Peak expression observed within 06-12 hour embryonic stages.
Coordinates
chr3R:16569485-16571044:+
Coord C1 exon
chr3R:16569485-16569682
Coord A exon
chr3R:16570941-16570943
Coord C2 exon
chr3R:16570944-16571044
Length
3 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGC
5' ss Score
5.61
3' ss Seq
AACTTCTGTCTCGCCCCTAGCAG
3' ss Score
7.29
Exon sequences
Seq C1 exon
GGCACGGATGGCATTCCCGGGCAGGAGGGGCCACGCGGGGAGCAGGGCTCCAGAGGGGATGCCGGCCCGCCCGGCAAACGGGGACGGAAAGGAGATCGCGGTGACAAGGGCGAGCAGGGCGTGCCCGGACTGGACGCCCCCTGCCCCCTCGGCGCCGATGGGCTGCCGCTGCCCGGCTGCGGATGGCGGCCGCCAAAG
Seq A exon
CAG
Seq C2 exon
GAAAACTGGCAGGCCTGGCTCAAGGACGAGCTAAATGCGCTGCAGCATCCGCGCTCAAAAAACTAATTGCCAGCGACCACCCCTCGGCGGCTGCAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0259244-22-24,22-23-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(23.5=24.2),PF0139113=Collagen=PD(77.5=83.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0292667
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0289172, FBpp0293542, FBpp0293543, FBpp0307753, FBpp0307754, FBpp0307755, FBpp0307756, FBpp0307757, FBpp0307758
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:
TGACAAGGGCGAGCAGGG
R:
GCCAGGCCTGCCAGTTTTC
Band lengths:
116-119
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)