Special

DmeALTD0009094-2/2 @ dm6

Alternative 5'ss

Gene
FBgn0052423 | shep
Description
The gene alan shepard is referred to in FlyBase by the symbol Dmelshep (CG32423, FBgn0052423). It is a protein_coding_gene from Dmel. It has 9 annotated transcripts and 9 polypeptides (6 unique). Gene sequence location is 3L:5155821..5277944. Its molecular function is described by: RNA binding; mRNA binding. It is involved in the biological process described with 7 unique terms, many of which group under: response to gravity; response to abiotic stimulus; response to stimulus; anatomical structure development; behavior. 65 alleles are reported. The phenotypes of these alleles manifest in: cellular anatomical entity; appendage; adult segment; adult tagma; nervous system. The phenotypic classes of alleles include: increased mortality during development; increased mortality; phenotype; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages, during late larval stages, at stages throughout the pupal period, in adult female stages.
Coordinates
chr3L:5166935-5168302:-
Coord C1 exon
chr3L:5168250-5168302
Coord A exon
chr3L:5168244-5168249
Coord C2 exon
chr3L:5166935-5167059
Length
6 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTT
5' ss Score
7.64
3' ss Seq
CAAAATATGCTTTTTTGCAGGTT
3' ss Score
7.58
Exon sequences
Seq C1 exon
ATACGGAACAATTATATCAACCAAGGCTATTTTAGATAAAACAACAAACAAAT
Seq A exon
GTAAAG
Seq C2 exon
GTTACGGCTTCGTCGACTTCGAGCAGCCAGCCTTCGCCGAGTGCGCCGTAAAAGGATTGCAGGGGAAGGGCGTGCAAGCTCAGATGGCCAAAGTGGGTATCTGGGTGCTTCATAGGCCGGCCATT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0052423-32-17,33-17-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact

Protein isoform when splice site is used (Ref)

No structure available
Features
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.015
Domain overlap (PFAM):

C1:
PF0007617=RRM_1=FE(27.3=100)
A:
NA
C2:
PF0007617=RRM_1=PD(40.9=64.3)


Main Inclusion Isoform:
FBpp0301014


Main Skipping Isoform:
FBpp0076876


Other Inclusion Isoforms:
FBpp0076875, FBpp0290814, FBpp0305482, FBpp0305483, FBpp0305484


Other Skipping Isoforms:
FBpp0076877
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:
CGGAACAATTATATCAACCAAGGCT
R:
AATCCTTTTACGGCGCACTCG
Band lengths:
108-114
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)