HsaINT0068092 @ hg19
Intron Retention
Gene
ENSG00000148288 | GBGT1
Description
globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 [Source:HGNC Symbol;Acc:20460]
Coordinates
chr9:136031288-136031452:-
Coord C1 exon
chr9:136031402-136031452
Coord A exon
chr9:136031324-136031401
Coord C2 exon
chr9:136031288-136031323
Length
78 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
CTGGTCCTTCTTGGTTGCAGGTC
3' ss Score
9.31
Exon sequences
Seq C1 exon
CAACATGAAGCTGCACTACAAGAGGGAGAAGCCACTCCAGCCCGTGGTATG
Seq A exon
GTAAGGAGACTGGCATTTCCTCTTTTGTGGCCGTGAGGGTGGTGGCTCTCCTCCATCACTGGTCCTTCTTGGTTGCAG
Seq C2 exon
GTCACAGTACCCTCAGCCCAAGCTGCTGGAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148288-GBGT1:NM_021996:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.079
Domain overlap (PFAM):
C1:
PF034148=Glyco_transf_6=FE(15.2=100)
A:
NA
C2:
PF034148=Glyco_transf_6=FE(10.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATGAAGCTGCACTACAAGAGG
R:
CTTGGGCTGAGGGTACTGTGA
Band lengths:
71-149
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)