DmeINT0027021 @ dm6
Intron Retention
Gene
FBgn0025802 | Sbf
Description
The gene SET domain binding factor is referred to in FlyBase by the symbol DmelSbf (CG6939, FBgn0025802). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3R:11789293..11796948. Its molecular function is described by 6 unique terms, many of which group under: binding; protein binding; enzyme binding; phosphatidylinositol 3-kinase catalytic subunit binding; Rab guanyl-nucleotide exchange factor activity. It is involved in the biological process described with 8 unique terms, many of which group under: vesicle-mediated transport; mitotic cell cycle; internal peptidyl-lysine acetylation; establishment of localization in cell; heterocycle biosynthetic process. 15 alleles are reported. The phenotypes of these alleles manifest in: fat body; autolysosome; macrophage. The phenotypic classes of alleles include: some die during pharate adult stage; viable; female semi-sterile; starvation stress response defective; lethal - all die before end of P-stage. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of low expression. Peak expression observed at stages throughout embryogenesis, at stages throughout the larval period, at stages throughout the pupal period, in stages of adults of both sexes.
Coordinates
chr3R:11796381-11796948:-
Coord C1 exon
chr3R:11796844-11796948
Coord A exon
chr3R:11796495-11796843
Coord C2 exon
chr3R:11796381-11796494
Length
349 bp
Sequences
Splice sites
5' ss Seq
GAGGTGTGT
5' ss Score
6.14
3' ss Seq
TCAACTCTTTGTTCTCCTAGATT
3' ss Score
8.03
Exon sequences
Seq C1 exon
TGCATCTATCTTTTTCTATGCGAACTTAAAAATAATTATTATAGCCCCGAATTCTTTGAGATTTGCTGGCAGTTAGCGGGGATTTCGGCTGCAGCCGGCTGCGAG
Seq A exon
GTGTGTGCGCGGATATATATATATAGATTGGCCAGTCCGATTCCCGGCGAACGATCCCACTTTGCGTGGCGGGGTGTGGTTAAAGAAAAAAGAGTGAAGACCAAGACTCGTAAAGCCTGAAAAACGCCTCCGGGCGCTATAGACAATACAATAACAATTCGGCCCCTCGATCTCCGTGGAGCTAATCATTTATGCCGAGCGCAGAGACGGAGCCTAATTAGCATATCAAATTGGATGACGGCACTGGCGAATAGAATCCATCTGCCGCTGTCCCCTGCTACAAGAACGCAACAGAACAAAAACAAAAAAAAAATCAAAATAAAACATCTTCAACTCTTTGTTCTCCTAG
Seq C2 exon
ATTTGGCTAGTAAAGAGCCGTAGGATCCTAGACGACTGGCCGGCTATGTGGTGGGCAAGATGTCCCGGCTCGCTGATTACTTCGTAATAGTCGGCTACGACAGTGATAAGGAGA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0025802:FBtr0082529:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0082003, FBpp0082004
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:
TGCATCTATCTTTTTCTATGCGAACT
R:
TCCTTATCACTGTCGTAGCCGA
Band lengths:
217-566
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)