HsaINT0068094 @ hg19
Intron Retention
Gene
ENSG00000148288 | GBGT1
Description
globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 [Source:HGNC Symbol;Acc:20460]
Coordinates
chr9:136028340-136030699:-
Coord C1 exon
chr9:136030565-136030699
Coord A exon
chr9:136029649-136030564
Coord C2 exon
chr9:136028340-136029648
Length
916 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
GACCGGGTGATCATCACTAGGTA
3' ss Score
4.08
Exon sequences
Seq C1 exon
GCCCACACAGCTGCTGACACTCACACCCTGGTTGGCGCCCATCGTCTCCGAGGGAACCTTCAACCCAGAGCTTCTGCAGCACATCTACCAGCCACTGAACCTGACCATTGGGGTCACGGTGTTTGCCGTGGGGAA
Seq A exon
GTGAGTAGTGGGCTGGGGAAGGGGAGGGAGGTCTCCCTGAGCCACAGGAGTTTATAGTTGGGAAGAGACCAGACCAGACGTGCACACAGGACCCTGCTGGGCACCCGGGAGGCTCGGAACCAGGTGCCAAGCAGATAGAAAGTACAGTGTAGGGTGTGATAGTGGGATGGGAGCTTCCTGGAGTAGGGGATCTGGCTCTAGCATAGACAGGATGCAGAGTCCAGGTGAGGGGACAGCAGGAGCCTTTGTCAGGAGGCCCCCTTGCCCCTCCCTGTTTCATCTAGACCCCTCCTCTGCCCTTGTCTCTCCCATGACCCCACCTGGCCTTCCTTTAGGAGCTGCCGCTTGGCAGCCTTCCTCTGGGCCTCTGGGACTCCTTCCTGGAACTTCCTGGGGCCCTAAAGCATGACCAGATGATGAATGGTCCACCTAGGGTCAGGTGACCCCCTTGTCCAATGAGTTTTGGCCTGGGGGCAGGGCTGTGTCAACCACACCCCCCTCCATGCCCCCAGCATCTAGCTCAACTTGCCTTCCCTTGATTCGTCCACTTACCTGCTTCTTCACTACTTTCTTCTCTGTGATCCTCAATGTTCCTGCCTGTAAAATGGGCATGCTTATGCAGATCAAAGATCATAAGAATTCTTAGAACGTCGCTGGGCACTTAGAAATTGCTCAGTAAAAGTTCACCTGGCCTAGGAGCATAAGAATCTCTACCAGGAACATGCTTACAACAGCCGTAAGAGGCTGGTACTAGCATTTTGGGAATTGGACAAATGAGGACCCAGAGGGCCAGAGCAGAGTGACATCTTGAGATGGGGAGCTGGTAAGTGGACCCCAGCCTGGCTGACCCCAGCACACAGTGGGGACCCTGGCAGGCTGCTGGTGTAGCAGTGGGTGACCGGGTGATCATCACTAG
Seq C2 exon
GTACACTCATTTCATCCAGTCCTTCCTGGAGTCAGCCGAGGAGTTCTTCATGCGTGGGTACCGGGTGCACTACTACATCTTCACTGACAACCCTGCAGCCGTTCCCGGGGTCCCGCTGGGTCCCCACCGGCTTCTCAGCTCCATCCCCATCCAGGGTCACTCCCACTGGGAGGAGACATCCATGCGCCGGATGGAGACCATCAGCCAGCACATTGCTAAGAGGGCTCACCGGGAGGTGGACTACCTCTTCTGCCTTGATGTGGACATGGTGTTTCGGAACCCGTGGGGCCCTGAGACCTTGGGAGACCTGGTGGCTGCCATTCACCCAAGCTACTACGCCGTTCCCCGCCAGCAGTTCCCCTATGAGCGCAGGCGTGTTTCCACTGCCTTTGTGGCAGACAGCGAAGGGGACTTCTATTATGGTGGGGCAGTCTTCGGGGGGCAGGTGGCCAGGGTATATGAGTTTACTAGGGGCTGCCACATGGCCATCCTGGCGGACAAGGCCAATGGCATCATGGCTGCCTGGCGGGAGGAAAGCCACCTGAACCGTCACTTCATCTCAAACAAGCCGTCCAAGGTGCTGTCCCCCGAGTACCTCTGGGACGACAGGAAGCCCCAGCCACCCAGCCTGAAGCTGATCCGCTTTTCTACACTGGACAAGGATATCAGCTGCCTGAGGAGCTGACCACGGAGCTGGGGGTTGCCATGGATGGGGACCCAAAGACCTGCAGCCACCAGTGCTTCACTAGCGTGCAGACCAGCCCTGTCCCGCCTCCCTGTCAGTCAGGCGAATTCAACCGGAAAAGGGACGTGGAAAGGCCACTGTGAACTGCAGAGGGCTGTGCACACAGTAGCACACAGGATCTCACAGTAACGCGGCATGGGAACAGTGAGACAGGGGGAGGGGAGGCGCAGTTACAAAGGCAGGGCCCGGCAGGCTTGCCACGTTCTGCAGCCGTGCCTTTGCGGGGCAGGCTCTGAAGCCTCAGCCCGACTCAGAGTGCCTGAACCCTGCCGCGCCAGTCCCCCGTTTATTGCATATTGCCCTTAACGTAGCATTTCTAATACCCTGGTGTGAAGGCGCCCTAGACCCCTTTTCTCTGGTCACAGGGGTCCTGGGTCCTTTGATGTCTCCCAACCACATGTAGCCAATTCCTCACTCAGGCCCCCAGAGTGAGCCTTTGAAATGGAACAGGTCTAGGCTCCCTCGGTTTCCTGCACCCCAAAGTGAGCCGCACTCTCAGGGGACTAGCCACCTCCTTCTTAAGAGGGTTTGGGGCAGTTTATAATAAAGGGGGCGTGTGCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148288-GBGT1:NM_021996:6
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.018
Domain overlap (PFAM):
C1:
PF034148=Glyco_transf_6=FE(40.2=100)
A:
NA
C2:
PF034148=Glyco_transf_6=PD(67.4=99.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGACACTCACACCCTGGTTG
R:
CGGTGAGCCCTCTTAGCAATG
Band lengths:
353-1269
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)