DmeINT0035237 @ dm6
Intron Retention
Gene
FBgn0031681 | pgant5
Description
The gene Polypeptide N-Acetylgalactosaminyltransferase 5 is referred to in FlyBase by the symbol DmelPgant5 (CG31651, FBgn0031681). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 2L:5072170..5093592. Its molecular function is described by: polypeptide N-acetylgalactosaminyltransferase activity. It is involved in the biological process described with: oligosaccharide biosynthetic process. 17 alleles are reported. The phenotypes of these alleles manifest in: embryonic/larval copper cell; embryonic/larval gut. The phenotypic classes of alleles include: viable; lethal; partially lethal - majority die. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed during late pupal stages.
Coordinates
chr2L:5077535-5078092:-
Coord C1 exon
chr2L:5077774-5078092
Coord A exon
chr2L:5077713-5077773
Coord C2 exon
chr2L:5077535-5077712
Length
61 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
GCCTCCTTAATCCGCTTTAGGTA
3' ss Score
7.82
Exon sequences
Seq C1 exon
ACTTTCTGGGCAAGCAGTTGGAGGAGTATGTGGCCAAATTGCCAGTTAAGACATTTGTGCTGCGTACAGAGAAGCGTTCGGGACTGATCCGAGCACGTCTCCTGGGTGCCGAGCATGTGAGCGGTGAGGTCATCACCTTCCTGGACGCCCATTGTGAGTGCACAGAGGGCTGGCTGGAGCCTCTGCTCGCGCGGATTGTGCAGAATCGTCGAACGGTTGTGTGCCCGATTATTGATGTGATTTCCGATGAGACATTCGAGTACATTACGGCCTCGGATTCCACGTGGGGCGGCTTCAACTGGAAGCTCAACTTCCGATG
Seq A exon
GTGAGCGAAAAGTTTCCTGGTTAGCGTAATCCCTTTAAAATGCCTCCTTAATCCGCTTTAG
Seq C2 exon
GTACCGAGTGCCATCGCGGGAAATGGCGCGCCGGAATAACGATAGGACTGCTCCGTTGCGAACTCCGACCATGGCCGGTGGTCTGTTCTCCATCGATAAGGATTACTTCTATGAGATTGGCTCCTACGACGAGGGCATGGACATTTGGGGCGGCGAAAATCTGGAGATGTCGTTCCGT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0031681:FBtr0079026:5
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=0.100
Domain overlap (PFAM):
C1:
PF0053521=Glycos_transf_2=FE(57.3=100)
A:
NA
C2:
PF0053521=Glycos_transf_2=PD(19.5=60.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0078663
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0110323
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:
CATTACGGCCTCGGATTCCAC
R:
GAACAGACCACCGGCCATG
Band lengths:
145-206
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)