MmuINT0069468 @ mm10
Intron Retention
Gene
ENSMUSG00000034807 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:MGI Symbol;Acc:MGI:1924348]
Coordinates
chr8:71610998-71612194:+
Coord C1 exon
chr8:71610998-71611444
Coord A exon
chr8:71611445-71612083
Coord C2 exon
chr8:71612084-71612194
Length
639 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGC
5' ss Score
6.64
3' ss Seq
TGTCCTGTCTGTGCTCACAGGGT
3' ss Score
10.42
Exon sequences
Seq C1 exon
GTCGGCGGAAAGCAGTGGAAGCTTTTAAAGGCGTAGCCTTGTCATGCCTCTCTCCAGGACTCACAGTATGACCCGCGGGCCACTTCCCTTTAAGGAGCGTGTCAGGGGTGGGACCTGGATGTGTCCTTCCCGCCGCCGACTCCTTTAAGGCGCGGCCCTCGTCCCCCGGCAGAAAAGCTGCTTAAAGGCGACGCGTGGCGCGATGGCGGCGTTGCCACGCGGGTCACGCGGGCTGCCGCTGCTGCCACTGCTCCTACTGCTGCCGCCGCTGGGCGGCCCGCGCGGCGCGGACGGCTACTTTCCAGAGGAGCGCTGGAGCCCCGAGTCCCCGCTACAGGCGCCGCGCGTGCTCATCGCGCTGCTGGCGCGGAACGCGGCACCCGCGCTGCCCGCCACGCTGGGCGCCCTGGAGCAGCTGCGCCACCCACGGGAGCGCACGGCGCTGTG
Seq A exon
GTGAGCTGCGGGCCCTTGCGCGGTGCACCGGGACTAGGCGGGACTCAAGTCTCTACCGGAGGGAGGTTGCTATGCACTTGGGCTCGGCTGTGCGCTGCGGAGACTCGGTCCTCTTTCTGAGGACCTGAGTTATGTACCCCAGGGATTACGCACTTGAGGGGGCTCGGCTCTATATCCATAGTGCCCGGGCTCGTCCCCACTGCGGCTTGGGACCCCAAGCTGCTGCCTCCTCCCCTCAGGTACTTAGGAATCTGTTCTGATTTGCTGCCAGCCCTCACAGCGAGCTACCATCCTAGAACCTCTGACTCCTTAGAATGGGCCAGGCTGGTGCTTCCAGACCCTTATAGCGAACTCCGGGACTTCCAGATAAGATTCCTGAGGCTCGGGCCAGCATTCCACGCTAACAAAGTTAATGAACTTATCTTTGTGACAGGGTCTCACACCAATGTGCTTTCCAAACCAGCAGGTTCTGTTCAGTTGTGTACTAGTGAGCTGGGTGTCATCTTTACTCCCCTGTCACCGATGGATGGGCAACAGGCTTGGAGTGTAGCGAGTTTTATCCAGGGTGTTATAGCTGATGGGTCTGAGCCAGGTTGGGAAACCCCCAGTGCCATCATCTTGTCCTGTCTGTGCTCACAG
Seq C2 exon
GGTGGCCACAGATCACAACACTGACAACACTTCAGCCATACTTCGAGAGTGGCTGGTGGCAGTGAAGGGTTTATACCACTCTGTGGAGTGGCGACCGGCAGAGGAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034807:ENSMUST00000047903:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.159 A=NA C2=0.158
Domain overlap (PFAM):
C1:
PF137041=Glyco_tranf_2_4=PU(21.5=31.7)
A:
NA
C2:
PF137041=Glyco_tranf_2_4=FE(30.6=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:
GACCTGGATGTGTCCTTCCCG
R:
AGTGTTGTGATCTGTGGCCAC
Band lengths:
358-997
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