DmeINT0011140 @ dm6
Intron Retention
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:16550861-16551667:+
Coord C1 exon
chr3R:16550861-16550929
Coord A exon
chr3R:16550930-16551613
Coord C2 exon
chr3R:16551614-16551667
Length
684 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTG
5' ss Score
7.76
3' ss Seq
GGTATGGTTGACGCTGTAAGGAC
3' ss Score
-3.36
Exon sequences
Seq C1 exon
GGTCTGAAGAGATCGGTGACAACGCTGCATGGCGGCACGCTGGGCTATGCGGAGATAGTTGCTGTTAAG
Seq A exon
GTATTGCCACCACCCACTCATCAACCGTACTCTTTGCCACTTGGGCTCCCCTTTCTTTGTTATACTTTAGACGTTGGCATGGTCAAGACCATTTTTCAGGGGCCAAATGCAGATGGCCCAGAGATGGCAGCCCGTAGCATACAACAAATTATTTGCAACTTGTTGTCCTTGGCTGAATCGCTCGGTTTCTGGATTTGTCCTTCTGGTCCAGTCATCGTAGTCCTCTCGTCCTTTTACTTAGTTGTGTAGAGTTGTGTTTATTGTCTCGCTTAATTCTCGTTTGTAATGCTTTTAAGTTGTCTCCTGTCTGTTGTCCTGTTGTGCTGCTGCCTTGGCTCTTTTGTTTAAACTGCGCCATAAATTCGTTGCAACATCGTAGTTTGGTAGACTTTCCCTTCCCACTTTCTTTTCCTTTGGCAGCGGCAAGTTTTCGGACAGATCTCTTGGTAGTTTTTAATGGAATTTCCATCCTATTTGTTTCGTAGTTTTGAGTTACCCTTTAAGAACATTTAATTTGGATTATTTGCTTTTAATTTGGCTAATCTAGCTTTTGCAGCAGCTGAAACTAACTTTATTTTGATGATTTATTAACCATTGTTTTTGAATAACCCATTTGGTTTTTTAATATATTTTTATATTTACATTAAAACTTGTTGTTTTGGTTGGTATGGTTGACGCTGTAAG
Seq C2 exon
GACTTGCAAGAAGCAGGCGTCAATGTATCCGCTTCCACAGTCATAAAGCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0259244:FBtr0299894:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.984
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(3.5=13.0)
A:
NA
C2:
PF0139113=Collagen=PU(1.2=5.6)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0292667
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0289172
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)