HsaINT0069708 @ hg38
Intron Retention
Gene
ENSG00000130309 | COLGALT1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:HGNC Symbol;Acc:HGNC:26182]
Coordinates
chr19:17577361-17578089:+
Coord C1 exon
chr19:17577361-17577467
Coord A exon
chr19:17577468-17577956
Coord C2 exon
chr19:17577957-17578089
Length
489 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
CCTCTCCTCCTCCTCTCCAGAGC
3' ss Score
10.06
Exon sequences
Seq C1 exon
GTCTTCATGATCAACCTGAGGCGGCGGCAGGACCGGCGGGAGCGCATGCTGCGGGCGCTGCAGGCACAGGAGATCGAGTGCCGGCTGGTGGAGGCCGTGGACGGCAA
Seq A exon
GTGAGTCCGAGGCCTGGGGGTGGGGGGGCGGGTCCGCACGTGGATGTGGGTGTAGACCTCGCTGGTAGACGGCAAGTGATTCAGATGGGGGCGGGCGTGGTGTCCAAACAGATGTAGACCTCGTCAGTGGGCGTCCTGAAGGGGAAGTGAATGGGACCCTGGGGAAGGGGCAGATCCTCACAGTTGTAGACCATGGAAGGCAAGTGAGTCCTGACCCAGGGGAATGGGTAGGTTTGCATGCTGCCAGTGTAGACTGGTGGGGACTGTGGAGGGGTAAGTCAGTCAGACCCCAGGAGAGGAGGAGAGCAGGTTTGCCCGCGAGTGTATACCATGTGCAGGTGAGTGAGGCCCCATGTGCCCGGAAGGGGTGCCAGTGCTACAAGAGGTGGACCAGCTGCTCAACGCCGCAGGGGGTGGTGGAATGGCCGGGGATGGCAGAATGGCAGGCAGGGTGAACCTTCTTCGTGACCCTCTCCTCCTCCTCTCCAG
Seq C2 exon
AGCCATGAACACCAGCCAGGTGGAGGCGCTGGGGATCCAGATGCTGCCTGGCTACCGGGACCCCTACCACGGCCGGCCCCTCACCAAGGGTGAGCTGGGCTGCTTCCTGAGCCACTACAACATCTGGAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130309:ENST00000252599:8
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:
PF0175512=Glyco_transf_25=FE(18.8=100)
A:
NA
C2:
PF0175512=Glyco_transf_25=FE(23.7=100)
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:
CTTCATGATCAACCTGAGGCGG
R:
CTCCTTCCAGATGTTGTAGTGGC
Band lengths:
238-727
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development