Special

DmeINT0036296 @ dm6

Intron Retention

Gene
FBgn0040918 | schlank
Description
The gene schlank is referred to in FlyBase by the symbol Dmelschlank (CG3576, FBgn0040918). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (1 unique). Gene sequence location is X:6257668..6267228. Its molecular function is described by: N-acyltransferase activity; DNA binding; sphingosine N-acyltransferase activity. It is involved in the biological process described with: SREBP signaling pathway; triglyceride metabolic process; negative regulation of lipid catabolic process; positive regulation of lipid biosynthetic process; ceramide biosynthetic process. 30 alleles are reported. The phenotypes of these alleles manifest in: prothoracic gland; terminal bouton; wing; endosome; trichogen cell. The phenotypic classes of alleles include: visible; lethal; increased mortality during development; phenotype. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed at stages throughout embryogenesis, during late larval stages, during early pupal stages.
Coordinates
chrX:6266407-6267228:-
Coord C1 exon
chrX:6267004-6267228
Coord A exon
chrX:6266718-6267003
Coord C2 exon
chrX:6266407-6266717
Length
286 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGCA
5' ss Score
6.28
3' ss Seq
ATACAATTGCGAATATTTAGAAA
3' ss Score
1.18
Exon sequences
Seq C1 exon
TGCAGTTACATTTACTGCTCCGCCGTCTCTGGGCACACTGTATTGTTGTTGCTCGACGAGGAAATACTATTAGTATTTTTTTTCGTTCATCCTGAAAGTTTAAGTGGACGAAACGAGCGGCGGCCGACTCGACACCGAGCCGAAATTCAGAAAGTCTATTGCTTTGGTCGAGAACAGATTGTCAGGGAACTTCACTTCATTTACGCTCCCAAACAAACGGCAAAG
Seq A exon
GTAGCATTTCCAAAAACGAATTAAATCGAAATCCAAATAGAAATAGAAGTAGAATTAGAAAAGCCATAAGCGCAAGTTAACGAGACAAGACAACAACAATTCGATTCGGCGGTTTTTGTTTTTTTGCCAGTGTGTGTTTGTGCTACGCTGTGAGTGTGCATTAGTGTCCGGTGCTCCTGTTGTTGTTCTTGTTGCTGTTGTTGTCGCTTATTGTTGTTCTTGCTGTTATTGTTGCTGTTGTTCGCAAGGCACAATAACACAGGCTCATACAATTGCGAATATTTAG
Seq C2 exon
AAAAAGCAAAGCATATACATATGTGACAACAAACGCCAAGGAAAAACTGGAAAGCTAAGCAAAGGAAAACCAAGAAAAAGAAAACAAACAATTGAGAAATTAAGAAGCGGCAACTGAAGCAGCAACATGGACATATTGAATGAGTTCAGCAATGTATTCTGGAGTACGCACATTTGGCTGCCGCCGAACACAACCTGGGCGGACATTGCGCCCGGCTCGCGTCCAGATGTGGTGCACGCCAACTACAAGGACCTCATATGGCCCATTCCATTCGCCGCTGTTGTCATGCTGGTCCGCTACACGCTGGAGCG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0040918:FBtr0070937:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact

5' UTR

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

C1:
NO
A:
NA
C2:
NO


Main Inclusion Isoform:
FBpp0070899


Main Skipping Isoform:
NA


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0070898
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:
TTAAGTGGACGAAACGAGCGG
R:
AGCCAAATGTGCGTACTCCAG
Band lengths:
305-591
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)