DmeALTA0006006-3/3 @ dm6
Alternative 3'ss
Gene
FBgn0010399 | Nmdar1
Description
The gene NMDA receptor 1 is referred to in FlyBase by the symbol DmelNmdar1 (CG2902, FBgn0010399). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 3R:5508842..5523328. Its molecular function is described by: NMDA glutamate receptor activity; signaling receptor activity; ligand-gated ion channel activity. It is involved in the biological process described with 12 unique terms, many of which group under: nervous system process; system process; regulation of biological quality; sensory perception of touch; response to external stimulus. 36 alleles are reported. The phenotypes of these alleles manifest in: larval dorsal multidendritic neuron ddaA; sensory dendrite. The phenotypic classes of alleles include: phenotype; neuroanatomy defective; partially lethal; behavior defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of extremely low expression. Peak expression observed within 18-24 hour embryonic stages.
Coordinates
chr3R:5516212-5523328:-
Coord C1 exon
chr3R:5523179-5523328
Coord A exon
chr3R:5516400-5516478
Coord C2 exon
chr3R:5516212-5516399
Length
79 bp
Sequences
Splice sites
5' ss Seq
ACGGTGCGT
5' ss Score
10.25
3' ss Seq
CTCCCCTTTTCGACTTGCAGAAA
3' ss Score
10.32
Exon sequences
Seq C1 exon
TTTTAGTAGACGAGCAACGCGCAAAGCGCCACGTTGTCCTTCACAGCCCCGGAAAAGCAAGGAAGGAAAAGCGGAAAAGCCAGGCGTCGCGTTGAGCGGGCGTCGAAAAGTAGGCAATACAGCTCTAGCTGCCTGCTGCCTGGTGCCACG
Seq A exon
AAAATGCTGGATGTTTGCTCGAGAAACCATTGAAATCGTTGCACAAAACACCTCGTTTATCCTCCCCCAGAAACTATAG
Seq C2 exon
ACTTCCGCATCATGGCTATGGCTGAGTTTGTTTTTTGCCGGCCATTGTTTGGGCTCGCCATTGTTCTCCTGGTGGCGCCAATTGATGCCGCCCAGAGGCACACTGCCTCGGATAATCCCTCGACGTACAACATTGGCGGCGTACTGAGCAATTCCGACAGCGAGGAGCACTTTAGCACCACAATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0010399-0-2,0-1,0-0-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.017
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0109423=ANF_receptor=PU(2.2=8.5)
Main Inclusion Isoform:
FBpp0078410
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
GGGCGTCGAAAAGTAGGCAAT
R:
GGATTATCCGAGGCAGTGTGC
Band lengths:
171-250
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)