DmeINT0018071 @ dm6
Intron Retention
Gene
FBgn0000299 | Cg25C
Description
The gene Collagen type IV alpha 1 is referred to in FlyBase by the symbol DmelCol4a1 (CG4145, FBgn0000299). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (1 unique). Gene sequence location is 2L:5029609..5037279. Its molecular function is described by: extracellular matrix structural constituent. It is involved in the biological process described with 8 unique terms, many of which group under: system development; cellular component organization or biogenesis; extracellular structure organization; tube morphogenesis; cellular component organization. 63 alleles are reported. The phenotypes of these alleles manifest in: adult circular muscle; intracellular membrane-bounded organelle; intracellular; epithelium; neuropil. The phenotypic classes of alleles include: phenotype; increased mortality during development; stress response defective; some die during larval stage. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of low expression. Peak expression observed within 12-24 hour embryonic stages, during early larval stages, during late pupal stages, in adult female stages.
Coordinates
chr2L:5029609-5030237:+
Coord C1 exon
chr2L:5029609-5029810
Coord A exon
chr2L:5029811-5030136
Coord C2 exon
chr2L:5030137-5030237
Length
326 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGG
5' ss Score
4.84
3' ss Seq
TCTCTGGCTCATCTTTCCAGGCC
3' ss Score
8.91
Exon sequences
Seq C1 exon
TATAATTAGTCGTGTTCCGTCTCCCCGAGTAAGTAGTAGTCTGGTCTCGGTCCGGAGCTGATCTGGCCAGCTGGTTTTAGTCTTTAGTCAGCGCTGTGGAGTGGTGATCGGTTCGGATCGGATCGCTCGGTTGTGAATGTGTGTTTCCATTAGGGTCCCGTCCCGTCCCGTCCAACCGTCCCTTAAATAGGATTTGATTCCT
Seq A exon
GTAAGGAACTGAGCTTTTACAACAACAAAATAATATAAACATAAAATATCTTAATTAAATCAGGAAGAACGCGTACTATTAATTGAAAATATCCAGCAAGTCGTTGTGCGAGTCTCGTACCAGTTCCAGTGCCTCTCAAACTGTCGCGTGTATATGCTTGGAAATGAAATGAAACGAAATACAAGAATTAAATCGTTGAAAAAAAATAAGCCAGCTCGATTTTCCCACAAATATTAAATAAAATAATATTCCTCTAAGAATATTTCCAATTTATTTTGCAACTGTTGCGAAATTAAAGTGCCCAATTCTCTGGCTCATCTTTCCAG
Seq C2 exon
GCCCAGCGACGGCAACATATAAACTTCAAATTCGACGAGGACAGAGCAAATAATTGTGCAGGCTTAAGTGCATAGGGCATCATGTTGCCCTTCTGGAAGCG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000299:FBtr0079003:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0078640, FBpp0078641, FBpp0078642
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:
ATAATTAGTCGTGTTCCGTCTCCC
R:
CGCTTCCAGAAGGGCAACAT
Band lengths:
302-628
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)