DmeINT0035227 @ dm6
Intron Retention
Gene
FBgn0027558 | pgant3
Description
The gene Polypeptide N-Acetylgalactosaminyltransferase 3 is referred to in FlyBase by the symbol DmelPgant3 (CG4445, FBgn0027558). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 2R:7057654..7061732. Its molecular function is described by: acetylgalactosaminyltransferase activity; polypeptide N-acetylgalactosaminyltransferase activity; transferase activity, transferring glycosyl groups. It is involved in the biological process described with 6 unique terms, many of which group under: biological adhesion; cell adhesion; transport; regulation of cell adhesion; oligosaccharide biosynthetic process. 15 alleles are reported. The phenotypes of these alleles manifest in: wing disc; wing blade. The phenotypic classes of alleles include: lethal; viable; visible; partially lethal - majority die; fertile. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of low expression. Peak expression observed within 12-18 embryonic stages.
Coordinates
chr2R:7060057-7060463:-
Coord C1 exon
chr2R:7060283-7060463
Coord A exon
chr2R:7060224-7060282
Coord C2 exon
chr2R:7060057-7060223
Length
59 bp
Sequences
Splice sites
5' ss Seq
TGAGCAAGT
5' ss Score
1.06
3' ss Seq
GCATTTCTTCTCCTGCGCAGATG
3' ss Score
9.37
Exon sequences
Seq C1 exon
ATGATTACAACATCAACCTGTTCCAGCCCATCAACGGAGAAGGTGCCGATGGGCGACCAGTTGTGGTGCCGCCTCGCGATCGCTTTCGCATGCAGCGCTTTTTCCGGCTAAACAGCTTCAACCTGCTGGCCAGCGACCGCATCCCACTGAACCGCACCCTCAAGGACTACCGCACACCTGA
Seq A exon
GCAAGTATAAGCCTTAGCTTACTGAGAACCTTTTCTAATGCATTTCTTCTCCTGCGCAG
Seq C2 exon
ATGCCGCGACAAGAAGTACGCCAGCGGTCTACCCAGCACGTCGGTTATAATTGTTTTCCACAACGAGGCCTGGTCCGTGCTCCTGCGAACCATCACCAGCGTCATCAACCGGTCGCCGCGCCACCTGCTTAAGGAAATTATCCTGGTGGACGATGCCAGCGATCGCT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0027558:FBtr0089061:3
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=0.018
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053521=Glycos_transf_2=PU(22.0=73.7)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0088130
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:
CGCTTTTTCCGGCTAAACAGC
R:
ATAACCGACGTGCTGGGTAGA
Band lengths:
134-193
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)