Special

DmeINT0029765 @ dm6

Intron Retention

Gene
FBgn0028646 | aralar1
Description
The gene aralar1 is referred to in FlyBase by the symbol Dmelaralar1 (CG2139, FBgn0028646). It is a protein_coding_gene from Dmel. It has 7 annotated transcripts and 7 polypeptides (5 unique). Gene sequence location is 3R:30445635..30455867. Its molecular function is described by: L-aspartate transmembrane transporter activity; L-glutamate transmembrane transporter activity; transmembrane transporter activity; identical protein binding; calcium ion binding. It is involved in the biological process described with 6 unique terms, many of which group under: transport; ion transmembrane transport; dicarboxylic acid transport; amino acid transport; localization. 17 alleles are reported. No phenotypic data is available. No phenotypic class data is available. 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 18-24 hour embryonic stages, during early larval stages.
Coordinates
chr3R:30449807-30450406:-
Coord C1 exon
chr3R:30450229-30450406
Coord A exon
chr3R:30449960-30450228
Coord C2 exon
chr3R:30449807-30449959
Length
269 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
CTTTGCAATTCTTCTTGCAGTCT
3' ss Score
9.04
Exon sequences
Seq C1 exon
ACTCGCAGTTAGTTAATCGCGGAACGAGGACGAGGTGGTTTCGACTCGGGCGGATTGGATTAGATCGGCTTGCATTGATGAGCTAATTAGACGCGGGAATTGCTCGCGGAAACAACACTGAACCAGAAGCAGTCAAAGCTAAAAAACAGGAATGCCGTTGACCAAGAGTTTGCCAAAT
Seq A exon
GTAAGTTTCAGCTGCGATTGCCAAGCGACTGACACGTGTTGCTTTTGCAATTGACTGTCAGGCGGGAGAGCGCAGAAATGAGAGTGCGACTGAGACAGTGGCGGGTAGCGAAGGGTTGTTTGTGAACTACCCATAAAGATAAAAGTATAAGTAAATACGTTCATATATACAGCAAAAAGATATTCAAAATAATCAAGTAGAGGAGAAGAAACCCCAATGAAGCAACCCTTTACCACAACTAATTATTTACTTTGCAATTCTTCTTGCAG
Seq C2 exon
TCTCCGTCGCTTTTGAAGCGCGCCGGCACCGAAAAGTTGCGAGAGGTGTTCCTGAAGTACGCATCCATCCAGAAGAATGGCGAGCACTATATGACCAGCGAGGACTTCGTGCGAAAGTTCCTGGGACTCTTTTCCGAATCTGCATTTAATGAC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0028646:FBtr0085694:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion (1st CDS intron)

No structure available
Features
Disorder rate (Iupred):
  C1=0.222 A=NA C2=0.007
Domain overlap (PFAM):

C1:
NO
A:
NA
C2:
PF138331=EF-hand_8=PU(47.1=47.1)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0303322


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0085056, FBpp0085057
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:
GAACGAGGACGAGGTGGTTTC
R:
TCGGAAAAGAGTCCCAGGAACT
Band lengths:
294-563
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)