DmeINT0030064 @ dm6
Intron Retention
Gene
FBgn0003890 | betaTub97EF
Description
The gene beta-Tubulin at 97EF is referred to in FlyBase by the symbol Dmel�etaTub97EF (CG4869, FBgn0003890). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3R:27967008..27988384. Its molecular function is described by: GTPase activity; GTP binding; structural constituent of cytoskeleton. It is involved in the biological process described with: mitotic cell cycle; microtubule cytoskeleton organization; microtubule-based process. 10 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: viable; fertile. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of very low expression. Peak expression observed within 18-24 hour embryonic stages, during early larval stages.
Coordinates
chr3R:27968927-27969827:-
Coord C1 exon
chr3R:27969660-27969827
Coord A exon
chr3R:27969192-27969659
Coord C2 exon
chr3R:27968927-27969191
Length
468 bp
Sequences
Splice sites
5' ss Seq
TCCGTGAGT
5' ss Score
8.93
3' ss Seq
GCTTTTCCTCACCCAACCAGGTC
3' ss Score
8.18
Exon sequences
Seq C1 exon
GTATCCGACACTGTCGTGGAGCCGTACAATGCCACGCTGTCCATCCACCAGCTGGTGGAGAACACCGACGAGACATTCTGCATTGACAACGAGGCTCTCTACGACATCTGCTTCCGCACGCTGAAGCTATCGTCGCCCACCTACGGCGATCTGAACCATCTCGTCTCC
Seq A exon
GTGAGTACCCCTAGTCAATCCATCTAATGCATCCTCTGTTTGTCTGTCCCATTTTCCCGTTTCCTGCTCCTACTCCTTCTGCTCTCCAATCGAAATCAATGGCGGAAAGGTGTCTGAGGTGGTGGTGGAGCCATATAACGCCACGTTGTCGCTGCACCAGCTAATTGTGGACACCGATGAGACGTTCTGCATCGACAACGAGGCTTTGTATGACATCTGCTATCAGAGCTTGCGCATCTGCTCGCCCACCTACCAGGATCTCAACCACCTGGTGTCAGTGAGTAGCCAAGACATTAGCATTAACGTGAAGCAAAGATGAAGATGAGGATAATGATGACCAGATGTCCACACCAGGAGCAATAAGTCCACCCTACCTTTCCCACAATCAAATCAAAAGAACAGAATTTGAAGTCCATGTAATCTGTAATTTTTTTCTGACAGTAATGTAGCTTTTCCTCACCCAACCAG
Seq C2 exon
GTCACAATGTCCGGAGTGACCACCTGCCTGCGCTTCCCTGGCCAGCTGAACGCTGATCTTCGCAAGCTGGCGGTGAACATGGTGCCCTTCCCGCGTCTGCACTTCTTCATGCCCGGATTCGCTCCGCTGACCGCCAAGGGATCCCAGCAATATCGCGCCCTCACGGTGGCCGAGCTGACCCAGCAAATGTTCGATGCCAAAAACATGATGACCGCCTGTGATCCCCGGCACGGACGCTACCTCACCGTGGCCTGCATCTTCCGGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0003890:FBtr0300611:4
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:
PF0009120=Tubulin=PD(22.1=87.5)
A:
NA
C2:
PF0395312=Tubulin_C=PU(47.2=65.2)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0289838
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
GTACAATGCCACGCTGTCCAT
R:
GCATCGAACATTTGCTGGGTC
Band lengths:
342-810
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)