GgaINT0124653 @ galGal4
Intron Retention
Gene
ENSGALG00000003340 | GBGT1
Description
globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 [Source:RefSeq peptide;Acc:NP_001025854]
Coordinates
chr17:6835767-6835940:-
Coord C1 exon
chr17:6835890-6835940
Coord A exon
chr17:6835803-6835889
Coord C2 exon
chr17:6835767-6835802
Length
87 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
ATATTTCTTCCTTTTCACAGATT
3' ss Score
10.14
Exon sequences
Seq C1 exon
CTCCAAGAAACTCCAGTATTTGGGAGATAAGCCAGTCCAGCTCTTCCCCCA
Seq A exon
GTAAGTATTAGCTTTTTATTTCCCATTGTTTCTCTCTTCTGGGCATATTTTGTGTATTATTCAATGGATATTTCTTCCTTTTCACAG
Seq C2 exon
ATTATTTTATCAGCAACCAAGAGTGCTGGCTCCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003340:ENSGALT00000005285:3
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=0.000
Domain overlap (PFAM):
C1:
PF034148=Glyco_transf_6=FE(5.0=100)
A:
NA
C2:
PF034148=Glyco_transf_6=FE(3.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTATTTGGGAGATAAGCCAGTCCA
R:
TTGGAGCCAGCACTCTTGGTT
Band lengths:
71-158
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]