MmuINT0069475 @ mm10
Intron Retention
Gene
ENSMUSG00000034807 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:MGI Symbol;Acc:MGI:1924348]
Coordinates
chr8:71619652-71620677:+
Coord C1 exon
chr8:71619652-71619771
Coord A exon
chr8:71619772-71620600
Coord C2 exon
chr8:71620601-71620677
Length
829 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CCCTCCTTTCTTACTCTCAGTGA
3' ss Score
9.15
Exon sequences
Seq C1 exon
AGGTGCAAATGTACGTGTGCAATAAGGAGGTGTACGGCTTCCTGCCCGTGCCACTGCGTGCGCACAGCAGCCTGCAGGACGAAGCAGAGAGCTTCATGCACGTGCAGCTGGAGGTCATGG
Seq A exon
GTGAGTCTCCTTGGGCCCTGGCCTCATTATCATGCATGCATCTCAAGAACTAATTGGGTACTGTTGGGTGGCAGTTCCTGTGTGTGGTGTGTGACTGAGGGAGACCATAGTCCCTGCCACTAGGGAGTTCTACAGTAGTCACAGGGTCAGCTGTCATCCTGGCAGATGCTGCCATACTCTTGTGTGCCTGTGCCCTTTGGTGTCCCCACACCACTGAGAAAACTGAAACATGAGCTGCTGTCTGTGGCACATGCCTGCCAACTTGGCAGTCTGGAGGCTGAGGCTGAGGCCCTGCATCCTGGGCTATAGCTTGAGACCATAGCCAAAAAGACTGCTCTTGTTTTGCAGCAAAGTTATTCTGTTCCTGAGGGTTGGTATACCTGTGTCGCTTTTAGGGGGTCGCATTTGGAGGGACAGCAGCCAGTGTGAACCTCACTGCATTTGTGTAAAGCTTCTGAGAGTTTCACTGAAGTTATCACACATGCACTGCTGGGATAATCCCTATGCATCTATTGAGTGCCTGCTGTTTACCAGGCACTGTTGGGCTCTGGGCATGCAATGTGTGTAGACAGATCCCACAGCCCTCCCAGGATGTTAGAGATGGAGTTAGAAAAGCAGGGATAGTGTCCTGATGGCCAAAGCCTGACACTTGGGCCAGAAGAGCCTGACCGGTCAGAGAGGCCTGGAGGCTCCCACTGGCTGGGCTGTCACAGCTGAGATCTGAGTTGCTCTGGGCAGGAACGTGGCAGGGGTGAAGGTCCTGGGGCATACCCTGGTTATACTGGGAGCTGGGAGAAGGGAGCATTGACCCCTCCTTTCTTACTCTCAG
Seq C2 exon
TGAAACATCCACCAGTGCAGCTCTCCCGATTCATCTCAGCACCCAGGAAGACTTCTGACAAGATGGGCTTCGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034807:ENSMUST00000047903:6
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:
NO
A:
NA
C2:
PF0175512=Glyco_transf_25=PU(1.1=7.7)
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:
AGGTGCAAATGTACGTGTGCA
R:
CGAAGCCCATCTTGTCAGAAGT
Band lengths:
192-1021
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