DmeINT0023482 @ dm6
Intron Retention
Gene
FBgn0026403 | Ndg
Description
The gene Nidogen is referred to in FlyBase by the symbol DmelNdg (CG12908, FBgn0026403). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (1 unique). Gene sequence location is 2R:10313891..10322104. Its molecular function is described by: calcium ion binding; extracellular matrix structural constituent. It is involved in the biological process described with: cell-matrix adhesion; basement membrane organization; regulation of basement membrane organization; basement membrane assembly involved in embryonic body morphogenesis. 31 alleles are reported. The phenotypes of these alleles manifest in: cellular anatomical entity; mechanosensory system; basement membrane; peripheral nervous system; larval thorax. The phenotypic classes of alleles include: fertile; semi-fertile; phenotype; locomotor behavior defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of very low expression. Peak expression observed within 12-24 hour embryonic stages.
Coordinates
chr2R:10318728-10319207:+
Coord C1 exon
chr2R:10318728-10318998
Coord A exon
chr2R:10318999-10319061
Coord C2 exon
chr2R:10319062-10319207
Length
63 bp
Sequences
Splice sites
5' ss Seq
TGAGTGAGA
5' ss Score
1.44
3' ss Seq
CCTATCATTGTACCTTGTAGTTC
3' ss Score
5.16
Exon sequences
Seq C1 exon
CGCTGCTCGAAGGACGCTGACTGTTACCAGGGCCGTTGCACGTGTCACGAAGGCTTCGACGGCGATGGCTACACCTGCACCAATATTTGCGGACATGGCGAAGTTTGGGAGAACGGACGTTGCGAGCCCCTGTTGCTCGAGAGGCATGATGTGGATCCGCTTTGCGATGCTCTAGGGGAATGCCGATGCCCCTATGGATACGAACTGAGCGAGGATAGCCAGCGCTGCACCTACGTGCAAGAATTCGATGGAGAAAGGAATGCCGATCTGA
Seq A exon
GTGAGATACTGTCAAGATAGGTGGAAGGCGTCGGGATTACTTACCTATCATTGTACCTTGTAG
Seq C2 exon
TTCCCTGCGATGTGGATGAAAACTGTCACATCAACGCCACCTGCAATTGGTATGGCCAGGAGCTTCGCCACATTTGCACCTGCCAGCCAGGATTCAGAGGCGATGGATACAACTGCGACCCAATCAGCGACGACTCCTGTGCAATT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0026403:FBtr0088349:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF129472=EGF_3=WD(100=75.5),PF129472=EGF_3=PU(5.3=4.1)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0087438

Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0308545
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:
ATGCCGATGCCCCTATGGATA
R:
GGTGGCGTTGATGTGACAGTT
Band lengths:
133-196
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)