MmuINT0069471 @ mm10
Intron Retention
Gene
ENSMUSG00000034807 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:MGI Symbol;Acc:MGI:1924348]
Coordinates
chr8:71612084-71613027:+
Coord C1 exon
chr8:71612084-71612194
Coord A exon
chr8:71612195-71612909
Coord C2 exon
chr8:71612910-71613027
Length
715 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CCATAGCTATTCCTTTGCAGCTC
3' ss Score
5.94
Exon sequences
Seq C1 exon
GGTGGCCACAGATCACAACACTGACAACACTTCAGCCATACTTCGAGAGTGGCTGGTGGCAGTGAAGGGTTTATACCACTCTGTGGAGTGGCGACCGGCAGAGGAACCCAG
Seq A exon
GTGAGCCTCAAATCCCCGACTGGAGTACTGAAGCTTGGGAAGGTAGGATCTAGAATGCTCCAGTTCTATCGTCAGCTTCCCCACCAGGTCCCTATCCTCTCAGCAGACCTTTGTCCCGTTGTCCTTCACTCCATTGTGCAACTTTGGACACAGCTGCCACACCTTTGTGGCTGAATTCCTTTGTGTCTGGTGGCTACCTACTGCTGTGTCTAGGGTCTTGCCAGCATCCACTCTCCTGTTTAACTTCCTGATAAGCCTGTCTTACTGTATAGTTCAGACTGAGGCCAGTTGCCAGCCTGTCTTATTGTGTAGTTCAGACTGAGGCAGTTGCCAGCCTCCTGTCTCAGTCTCCTGAGTGCTAGAATCACCCAGCACTACTGCATCAGGCTCAGAACCTGTAGGACAGTGTGCAATAATGTGTGTGCATGCTCACGCTCCTGTTCTCAGAGGCACTACGGTGGCCCCAGGCTCTCCCCAGCCATGCAGAGCTTTCCTTGGGTTTCAGCTTGCCAGTAGCTTTTGTGCCTCTGGACCCTTGCACATGCTGGGCTGGCATTTAGGCCCCTGTGTCCTGTCCCCCTCCCATGCTCCACACAGAGGTCTTCAGATCCACTTGCCTGCCACCTCTGTGAAGTCCTCTATGATCCCCTGTAACTGTGCTCTCTGGGTCCCCACGGTGCCCTATAATGTGCACACCATAGCTATTCCTTTGCAG
Seq C2 exon
CTCTTACCCAGACGAAGAAGGCCCCAAACACTGGTCCGATTCCCGCTACGAGCATGTCATGAAACTGCGCCAAGCAGCCTTGAAGTCAGCTAGGGACATGTGGGCTGACTACATTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034807:ENSMUST00000047903:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.158 A=NA C2=0.250
Domain overlap (PFAM):
C1:
PF137041=Glyco_tranf_2_4=FE(30.6=100)
A:
NA
C2:
PF137041=Glyco_tranf_2_4=FE(32.2=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:
GTGGCCACAGATCACAACACT
R:
GTAGTCAGCCCACATGTCCCT
Band lengths:
222-937
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