MmuINT0069476 @ mm10
Intron Retention
Gene
ENSMUSG00000034807 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:MGI Symbol;Acc:MGI:1924348]
Coordinates
chr8:71620601-71620854:+
Coord C1 exon
chr8:71620601-71620677
Coord A exon
chr8:71620678-71620747
Coord C2 exon
chr8:71620748-71620854
Length
70 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
CACTGAGGCTCTGGCTACAGGTC
3' ss Score
4.24
Exon sequences
Seq C1 exon
TGAAACATCCACCAGTGCAGCTCTCCCGATTCATCTCAGCACCCAGGAAGACTTCTGACAAGATGGGCTTCGATGAG
Seq A exon
GTGGGCTGGGGCCTCCTGGGTCGGGGGAGGCAGCCAACCTGACCCTGCCTCACTGAGGCTCTGGCTACAG
Seq C2 exon
GTCTTCATGATCAACCTGAAGCGGAGGCGGGACCGGCGAGAACGCATGCTGCGGGCACTACATGAGCAGGAGATTGACTGCCAGCTGGTGGAGGCTGTAGATGGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034807:ENSMUST00000047903:7
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=PU(1.1=7.7)
A:
NA
C2:
PF0175512=Glyco_transf_25=FE(18.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAACATCCACCAGTGCAGC
R:
CACCAGCTGGCAGTCAATCTC
Band lengths:
167-237
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types