DmeINT0023373 @ dm6
Intron Retention
Gene
FBgn0085434 | NaCP60E
Description
The gene Na channel protein 60E is referred to in FlyBase by the symbol DmelNaCP60E (CG34405, FBgn0085434). It is a protein_coding_gene from Dmel. It has 11 annotated transcripts and 11 polypeptides (9 unique). Gene sequence location is 2R:24891614..24921677. Its molecular function is described by: voltage-gated sodium channel activity; voltage-gated cation channel activity; cation channel activity. It is involved in the biological process described with: sodium ion transmembrane transport; neuronal action potential; olfactory behavior; membrane depolarization during action potential; sodium ion transport. 40 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: behavior defective; viable; smell perception defective; chemical resistant. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of very low expression. Peak expression observed within 06-12 and 18-24 hour embryonic stages, during early larval stages, during late pupal stages, in adult male stages.
Coordinates
chr2R:24911353-24912173:+
Coord C1 exon
chr2R:24911353-24911453
Coord A exon
chr2R:24911454-24911998
Coord C2 exon
chr2R:24911999-24912173
Length
545 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
ATCGATCATTTCTATTCCAGGTG
3' ss Score
9.1
Exon sequences
Seq C1 exon
GTATCAGTATTCTCGCTGCTTATTGAAGAGAATGAAAACCTTAAGGTCCTAAGATCGCTGCGCACATTACGAGCTTTGCGCCCGCTGAGAGCCATCTCTCG
Seq A exon
GTAAGTTGACCAATTATTGGTCTCCCGATAGGCTGCACCACAACCTTCTCAGACATACGTGCATCCGATGAAGAAAGCTATCTGCGTAGGAACTTCCGTCACTACTTCTCGTTCATTCTCTATCACTACTGATCTATTTTATCTTTTTGGGGAGGAGTTGGTCAGACCGAGCGATGCGATCCAAGCCGTGTGCAGTGTTTAATACAATCTCGTCTTCTTTATGAATTTCGAATAGAAATACGTACTCGTAGAACACGCATTGCATCGTCCTCGCCTCCGTCCTTGTCCTCGTCCCTTTAGTCTGTAGTTGAAGTATAGACCTTTCCTTTGCATCTGTAGTTTTCGTTTATTGTAGAAATAGAAAAGAAAAACATGTATATATGTTGGAAATAAGCTAGCTAAATAGTTGACTAAGCAGATAAGTTCCACTCCACCATCTATACACCATTTGACCACGACCACTTGGCACTTTCCCGGCATAGTTGAGACGACATGTGTCCATCACGTTATTGCTGCTGGCATTTCATCGATCATTTCTATTCCAG
Seq C2 exon
GTGGCAAGGAATGCGGATTGTAGTAAACGCTCTCATGTATGCAATACCATCAATTTTCAATGTTCTTTTGGTTTGTTTGGTTTTTTGGTTGATCTTCTCAATAATGGGTGTTCAGTTCTTTGGTGGTAAATTTTTTAAGTGCGTTAATGAGATGGGCGAGCTACTGCCGATTACT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0085434:FBtr0308342:17
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:
PF0052026=Ion_trans=FE(14.9=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(26.2=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0303273
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0300661, FBpp0300662, FBpp0300663, FBpp0300664, FBpp0300665, FBpp0300666, FBpp0305951
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:
TCAGTATTCTCGCTGCTTATTGA
R:
GTAATCGGCAGTAGCTCGCC
Band lengths:
272-817
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)