DmeINT0020458 @ dm6
Intron Retention
Gene
FBgn0031495 | GABPI
Description
The gene beta4GalNAcTB pilot is referred to in FlyBase by the symbol DmelGABPI (CG17257, FBgn0031495). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (2 unique). Gene sequence location is 2L:3030539..3032300. Its molecular function is described by: protein-cysteine S-palmitoyltransferase activity. It is involved in the biological process described with: protein targeting to membrane; endoplasmic reticulum to Golgi vesicle-mediated transport; protein palmitoylation; peptidyl-L-cysteine S-palmitoylation. 9 alleles are reported. The phenotype of these alleles manifest in: wing. The phenotypic classes of alleles include: partially lethal; viable; lethal; fertile. 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 00-18 hour embryonic stages, at stages throughout the larval period, at stages throughout the pupal period, in stages of adults of both sexes.
Coordinates
chr2L:3030539-3031893:+
Coord C1 exon
chr2L:3030539-3030947
Coord A exon
chr2L:3030948-3030999
Coord C2 exon
chr2L:3031000-3031893
Length
52 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
TAAAATTAAATTTACCACAGACT
3' ss Score
5.12
Exon sequences
Seq C1 exon
GCTGTGTTGTTGTAGTTGTCGTTATTCCGGAGAAATTGTAAGCAAATTCGTTGTACTCCAATAAAACAATTAAAATGGACCCACCCGGATCTGATAATTACTTTTGAAACATTTCTCCACTCGGCCAGTAGGGCGTGCACTAATCTAATCTAAACTGTTTCCGTACACGCTGCTCGGAACTCATTAAAAAACGTTCGCCGCGCCATTTCCTGTCCAAATCGATGTTCTTGATGACAGCCGGCACCTCCAATTTTCTTTCTGCAGCCTGGAGATCAGAGGCTGAGGAGTCCAAGAGTAAGGAGAACGGGAGTCTCTGCTGCTGCGAGTACGTGGCTGAGGACAGTCGAGAGCGATCCCACATCCTAGGATGCTGTTGTAACTGCGTGGACTTCGACTTAGTTTGCACAAG
Seq A exon
GTAGGATACATAAATGAAAGGCCGTCTACAATTAAAATTAAATTTACCACAG
Seq C2 exon
ACTTGTCACCTGCCGAGCCATTGATCGAAGGAACATCGACGGCATGCTCATCGCCTTCCAGGATAGACTGCGCTTGCCATGGCGCGGAGGAGCCAAGCGAATCTCGCCCGCAGCCGTTGCTCCCGCCTTCATTGTCCCCCTCATGCTGGGATTGGCCACTCTGAACTCAAAGACCGCCATAGTGCTGATGCTCACGCTGGTGGGCTTCACCATCTGGGGCATGGAGCTGGCTAAGCGGACCGCCACGCGGACAAACTTCTTTTTGAGCTGGCTGGTCTTCTCGGTGTTCTACATGATCATCATATTTGAGTTTCAGGTTCCTCTGCTGGAGCTGGCTCCGGAGGAGAACTACGCGTTAATGTTCTTCTCCTGTGCCGCTTTGTACTGCCTCTATTCCGCCAAGGCACTGTCGCCCTTGAATCTTGTTTCTGCTCAATACGGAACCACGCCCAAGGATGAGCTGCCTGGGATCGCCGAGGCTTCGAGTGGCGAGGAGCAGGCAGAGGCCCAGACCACACTCCAGATGGAGAGTGTGCTGAGTTTGGATGATGACGAGGTGGGGGATATGGACACTGCTGAGCGATCTGGCTTGATGCACGGTCAGCCCAATATCTGCGAGATCTGCCGGAAGGTTACTCCAAGGCGGGCATACCACTGTCCCGTCTGCGGAACCTGCGTGAAGAGGCGCGATCATCACAGCTACTGGCTAAACTGCTGCATTGGCGAGCGGAACTACGTGTGGTACATTGTTGGACTGGCCCTGTCGGAGATCGCTCTGCTGCTCGGCGCAAACTTGACCCTCACTTCCATTTGCCATCCGTTTATGGTGGTGCGACCGCTTGGTTATCCAGTTCTTTTGCCCGACGACTGCAGTGAGGTGTTCGAAGGCTTCGA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0031495:FBtr0077652:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=0.027
Domain overlap (PFAM):
C1:
PF0152915=zf-DHHC=PU(73.6=42.3)
A:
NA
C2:
PF0152915=zf-DHHC=PU(75.0=43.1)
Main Inclusion Isoform:
FBpp0311066
Main Skipping Isoform:
FBpp0077336
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0077335, FBpp0077337, FBpp0311067
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:
CGAGAGCGATCCCACATCCTA
R:
GCAGTCTATCCTGGAAGGCGA
Band lengths:
136-188
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)