HsaINT0069709 @ hg38
Intron Retention
Gene
ENSG00000130309 | COLGALT1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:HGNC Symbol;Acc:HGNC:26182]
Coordinates
chr19:17577957-17579609:+
Coord C1 exon
chr19:17577957-17578089
Coord A exon
chr19:17578090-17579481
Coord C2 exon
chr19:17579482-17579609
Length
1392 bp
Sequences
Splice sites
5' ss Seq
GAGGTGTGT
5' ss Score
6.14
3' ss Seq
GGCGGGGCTTCCTCCCTCAGGTG
3' ss Score
8.62
Exon sequences
Seq C1 exon
AGCCATGAACACCAGCCAGGTGGAGGCGCTGGGGATCCAGATGCTGCCTGGCTACCGGGACCCCTACCACGGCCGGCCCCTCACCAAGGGTGAGCTGGGCTGCTTCCTGAGCCACTACAACATCTGGAAGGAG
Seq A exon
GTGTGTCCTGAGTGATGGGCGGGGCCAGAGTTATGACTCTAGATCTCATCGGAGATTTGGACGGGAAAGGGGTTGAAAGAGTTCCCCAAAGCCCCGGCTAGGCATCCAGCCTCAGCCATGGGACCCATGGCCTCTCTTTAGTGAATGATGCGCCACACCAGCTGTATCACCCCCAGGTGTACCTGCCATCCTTCCATTGCGCAAATGTGGAAACTGAGCCTGGGGGTAGGGGTGAGCCCTTTTGAGCAGCAGGTGGTGTCTGGGGCCTGGGACCTGTAAACAAATCCTCATTACTCCCAGCCTGGTCTCTGTGCTTGATGTTTAGTACTAGAAGTCATGGCCACAGAGCCACTTTAAACCAGCACCTGCCCAGTGCTGCTGGGGGCACTCACCAGCCCAGGCATCCTCATCCACCCTCAGAGGGAGAGGCTGTGATTGGAGGAGGGTGTCTGACTAGGCTTCGAACTTGGGCCATCAGGGCCGGGCATGGTGGCGCACACCTGTGGTCCCAACTATTTGGGAGGCTAAAGTGGGAGAGTGGCTTGAGCCCAGGAGTTAAGGCTGCAGTCAGCCAAGATCGTGCCACTGCACTGCAGACTGGACAGCAGAGCAAAACCGTGTCTCAGAAAAAAGAAAAATGGCTGGGCGTGGTGGCTCATGCCTGTAATCTCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACCTTAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCTAGACTCTACTAAAAATACAAAAATTATCTGGGTGTGGTGGTGGGCACCTGTAATCCCTCTACTTGGGAGACTGAGGCAGGAGAATCACTTGAACCCAGGAGGCAGAGGTTGCAGTGGGCTGAAATCATGCCATTGCACTCCAGCCTGGGCGACAAGAGTGACACTCCATCTCAAAAAAAGAAAAATAAAATCCGGGCGTAGTGGCACATGCCTGTAATCCCAGCTGCTCAGGAGGCTGAGGCAGAATTACTTGAACCTGGGAGGCGGAGGTTGCAGTTGAGATCGTTCCACTGCACTCCAGCCTGGGCGACAGGGCGAGACTCCGTCTCAAAAAAAAAAAAAAAGAAAAAGAAAAGAAAAACTTGTTATCGAATGTGAAGCCAAATGGGGGTGTGCGGCTGCAAGGCGGGAGGTGCATGAGGCGTGGGCATTTGAGGGGCTGGGAGGCCTTTCTCTTCTGAGATCCATTATGGACGGCAGAGGGCAGAGGTTTGGATGTCCAGATGTCCCTGGAGCTAGGAGAGGCAGGGAGATGCACTGGCTTCTCTACGGGTCTTTCAAACCTTCTCAAAGCAAAGCTCTGTGCTTTAGGGTCAGGCCTGGCCTTGGCCTCCCTGTGATGTGGCGGGGCTTCCTCCCTCAG
Seq C2 exon
GTGGTGGACCGGGGGCTGCAGAAATCGCTTGTGTTTGAGGATGACCTGCGTTTTGAGATCTTCTTCAAGAGACGTCTGATGAACCTCATGCGGGATGTGGAGCGGGAGGGCCTGGACTGGGACCTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130309:ENST00000252599:9
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(23.7=100)
A:
NA
C2:
PF0175512=Glyco_transf_25=FE(22.6=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:
GCCATGAACACCAGCCAGG
R:
ATGAGGTCCCAGTCCAGGC
Band lengths:
260-1652
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