DmeINT0023762 @ dm6
Intron Retention
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:5511381-5512227:-
Coord C1 exon
chr3R:5512015-5512227
Coord A exon
chr3R:5511810-5512014
Coord C2 exon
chr3R:5511381-5511809
Length
205 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TTCCAAATTTCCGAACTCAGATT
3' ss Score
5.1
Exon sequences
Seq C1 exon
CATGATCGTGGCACCACTAACCATCAATCCGGAGCGTGCCGAGTACATTGAATTCTCGAAGCCATTCAAATACCAAGGCATTACAATACTCGAGAAGAAACCGTCACGATCGAGTACTCTCGTGTCTTTCTTGCAGCCGTTTAGTAACACGCTATGGATCTTGGTAATGGTGTCGGTCCATGTTGTGGCGCTCGTGCTCTACCTGCTGGACAG
Seq A exon
GTGAGTGAATCCTGGGGCTACCACCCCATCCCATCCCATACCCCCACCATACCACAAAAACCCACCCAAGCAAAAGTGTAGCGAAGCAGAGGGCTGCTGCATTGGACGGTTGAATGGCACCCCGACCAGCTAATCCCCGCCTGGAGTGGCCTGCAGATCCGGATCCTATTAACCACACGTTTCAATTCCAAATTTCCGAACTCAG
Seq C2 exon
ATTCTCGCCGTTCGGACGCTTCAAGCTCTCGCACTCGGACAGCAACGAGGAGAAGGCCCTCAATCTCAGCTCCGCGGTGTGGTTCGCCTGGGGAGTCCTGCTGAACAGCGGGATCGGCGAGGGCACGCCCCGGAGCTTCTCCGCCCGGGTGCTGGGCATGGTCTGGGCCGGATTTGCTATGATCATCGTTGCCTCGTACACCGCCAACCTGGCCGCCTTCCTCGTGCTGGAGCGGCCCAAGACCAAGTTGAGCGGCATCAACGACGCCCGCTTGCGGAACACCATGGAGAACCTGACCTGCGCCACCGTCAAGGGCTCCTCCGTGGACATGTACTTCCGTCGCCAGGTGGAGCTCTCCAACATGTATCGCACCATGGAGGCGAACAACTACGCCACCGCCGAGCAGGCCATCCAGGATGTGAAGAAGGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0010399:FBtr0078763:11
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:
PF0049715=SBP_bac_3=FE(20.5=100),PF0006021=Lig_chan=PU(8.5=31.9)
A:
NA
C2:
PF0049715=SBP_bac_3=FE(41.3=100),PF0006021=Lig_chan=FE(52.8=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0078410
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:
ATGGTGTCGGTCCATGTTGTG
R:
GATGCCGCTCAACTTGGTCTT
Band lengths:
306-511
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)