MmuINT0069470 @ mm10
Intron Retention
Gene
ENSMUSG00000034807 | Colgalt1
Description
collagen beta(1-O)galactosyltransferase 1 [Source:MGI Symbol;Acc:MGI:1924348]
Coordinates
chr8:71623090-71624911:+
Coord C1 exon
chr8:71623090-71623296
Coord A exon
chr8:71623297-71623492
Coord C2 exon
chr8:71623493-71624911
Length
196 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGA
5' ss Score
5.55
3' ss Seq
GTCTCTGCTATCTCCCATAGGTC
3' ss Score
11.73
Exon sequences
Seq C1 exon
CTACGTGGGCCGGAAGCGCATGCAGGTGGAGCACCCTGAAAAGGCTGTGCCCCATGTAAGGAACCTGGTAGAGGCTGATTACTCCTACTGGACGCTAGCCTATGTAATCTCCCTGCAAGGTGCTCAGAAGTTGCTTGCTGCCAAGCCACTGGCCAAAATGCTACCTGTTGATGAGTTTCTGCCTGTCATGTTTGACAAGCACCCAAT
Seq A exon
GTAAGAAGGCTATGAAGGGGTGGGTATTTGAGGGGGTTTGGGTGGCAGGCTCGGGTCTTTGAGTCTTGGAAGATCAGGGCAGGGGAGTGTTGGGCTCTGGCTAGGCATGGTGGGGTGAATCCTAGTGGACTCAAAGGAAAGTCTTTTTCTGGATCATTGGTCTCCATCTCCCCTATGTCTCTGCTATCTCCCATAG
Seq C2 exon
GTCAGAATACAAGAGTCACTTCTCTCCCCGCAACCTGCGTGCCTTCTCTGTGGAGCCCCTCCTTATCTACCCTACACACTACACAGGGGATGATGGCTATGTGAGTGACACAGAGACCTCAGTTGTGTGGAATAATGAGCAGGTTAAGACTGACTGGGACCGAGCCAAGTCCCAGAAGATGCGGGAACAGCAAGCACTGAGCCGTGAGGCCAAGAACTCAGATGTGCTCCAGTCTCCACTGGACAGCACTGCCCGTGATGAGCTTTGAGGCAACTGGCAAACAGCCAAAGCCACTGCTACACACCTAAACTTCATGTGCTTGCCTGGGACTATAGGGCCACTCAGGCAGACAACAGAGAGCTCTACAAGCACAGAGGTCTCCATGTCTTCCTGTTTAGCAGCCACTTACACACAGGCAGCATTTATGGAGTACTTACTGTATGCCAGAAATAGGGCTGACCACCAAGAGATTGGTCAGGAACAAGCACAGTCAGTTGGGTCCACCATGAAGGAAGTTCTCTTGTTAGAGCAATGAAAGAGGCATGATTCCCCCTTATCAGTGATGAACTGATCATCAGTCTTTTATTGTTCAGACTGAGTCAGGTATTAGGGATACATACTCATTTTTAAAATCCGTTTGAGTATTTATTGAGGGCTTACTGTATATTAGGTACCATTCTTAGCTCTGGGAATACTGAAATAAGAAAAAAAAATCAAGCAAAATATACCAAGCAGCTGCTATGTGCCAGGTCTTAGGAAGCACTGATGAGTTAAGTGTCTACTATGTGTCACTCAGTAGGTGCTGGAGATGGATGTCCCAGTGGTGCTTATCCTTGTAGTGGGCATGATATGCTTACGGTGGAAACAGTCTTATTGACCCTGTGTGCTAGGCTACACGCTGAGCACAATGACAGAGTCTAAACAGAATGTAACAAGCATTTATTGAGCACCTAGAGTATCAGGCCTTTGACTCCCAGTTGGTTGAGAAATAGCCACCCTCCAACCTGTCTGCCGGAGGACACTGGGCTTCCCTTGTCTAGAAGGGAGCATTGCTCTCCTTCCCTTGGTTGACTGCTAGGTTCAAGGATACTCATGACCTTGCAAGTCCCCCACCCCCCGTGTCCCTGGGCTGGGGCTCCCTTGCCCACCCCTTACTTCCAGAGCTTCTCTCTGCCCTTGTATCTCAGGTGTCCCTTGGCTGCTCATATGTTTGGGGCCTTGAGGTGCCCACCTGTATTGGGGTGCTCCTCTTGGCCTGAGCAGTGTGTTTACCAGCAGGCCAGGGTGTTGCTGTCCCTTCAAAACCAAATTGACTGTCAACTGGACAGTGGGTACCATCTTCTTGGGATGACTGCTTGCCTGCTCAGGTCTTGGTAACTTGCTCATGTTTGTATTAAATTCTTATTGGTTTTCACTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034807:ENSMUST00000047903:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.404
Domain overlap (PFAM):
C1:
PF0175512=Glyco_transf_25=PD(32.3=85.7)
A:
NA
C2:
NO
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:
CCACTGGCCAAAATGCTACCT
R:
GCATCTTCTGGGACTTGGCTC
Band lengths:
244-440
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