MmuINT0140002 @ mm10
Intron Retention
Gene
ENSMUSG00000016763 | Scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:MGI Symbol;Acc:MGI:1890616]
Coordinates
chr15:83616611-83618689:-
Coord C1 exon
chr15:83618552-83618689
Coord A exon
chr15:83616815-83618551
Coord C2 exon
chr15:83616611-83616814
Length
1737 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
GGGTTCCTTCACCCCTTCAGGCA
3' ss Score
6.92
Exon sequences
Seq C1 exon
ACAACTGCCACGTGACTTTTGTGACCCTCAAGTGTGACTCCTCCAAGAAGAGGCGCCGAGGCCGCAAGTCCCCATCCAAGGAGGTGTCCCACATCACAGCAGAGTTTGAGGTGGAGATGAAGGTGGATGAGGCCTCAG
Seq A exon
GTGGGTGATGTGTTCTTGGGGACTGGGGGGTCTGGCAGACGTGAGGCCGAGTGAGTCATAGAGAAGTCGGGGCTTTGGGAGGGGGGTACTGCACACTGCAGGGTGGGTACTACACACTGCAGGTCAAGCTCTGCAGCCCTGGGTTCAGGAGGCAGTTCGAGGTAACATTTGGAGCACAGCTAAGGGGCAGAGATGGCAAAGTACCCCAACTCTATGTGCCTGCTAGGGCAGGAAGGGCAGGGGCAGAGCCTCCCTATAGCAGCCAAACCAGGCCCTCTTTCCAACCAGTAAGAGAAACTTGTAATATGAGATTCATCCAGGCATTCCTTCTTAGCCCTAGGTGAGCGGTGGGTAATGGATGGGTTATTTGCTACTGTTATTATTATTGTTGTCATTGTTACTGTTGTTGTTGTTGTTGTTATCATTATTGGTCTTTTGGAGACAGGTTCTGTCTATTATGCTGCCCTAGCTATACTAGAACTCTCTGTTGTTGTTGTTGTTGTTAGTAGTAGTAGTAGTAGTAGTAGTCGTCGTCGTCGTCGTCGTCTTTTTGAGACAGGTTCTATCGATTATGCAGCCCTAGCTGTACTGGAACTCTCTATGTAGACCAGGATAGACTCAAACTCACAGAGATCCTTCTGCCTCAGCCTCCACAGTGCTGGGATTAAAGGTGTGCCCCACCAGGCCTAGCTTGGGTTGTTTGCTCTTAAGATGAGGTCTTATGTCGCTCAGGCAACCTTCAAAGCTGATAGGCAGCTAAGTATCATCTTCACTCCTCATCCTCCTGCCTCCACTTCTTGAATGCTGGGATTTCGGGCACATACCCACCCCTCCTGGCTCCAGTGGTAGGCAATGACAGAACCGGCTGCTGTTGGCAGCTGTGCTGTGGAAATGTGTGTCTGGTCCGGGCCATGGGCATCGTGGCCATGACCACCGCCCTAGAAGTACTCTCACCTGTGGAGAAGCAGATATGTGTGTGTCATCGGTGCTGGGCGAGAGTAGGTGGCAGGCCTGTGAGAATACATAGGCAAGGGGAGGTATGGGAAGCCTTCTAAACTAGAGACAGAAATCTAAAGTTTTCTGGTTGAAGTGGTGAGGAATGGGGTCCAGGAAGAGAAACCGAGCAGGTAGATGCACAGGGATCAGAGAGAACAGGACACTGTCACCCAGGGATCGGCAAGGAAGCAGAGCAAAGGCAAGCAGGAAGCAGAGAGAGACAGAGGGACCTAGGTCCCTACATCCTCTAGCTAAGCCATACCACCAAAGGAGTTCAGAACCTCTCCAGACGGCACTGCTAGCTAGGGGCCATGCCTTCAAACCTTTGTGGCAAGCAGGGGGTCAGGAGAGCTGTTACACATCCACCTGATTTTTATGTGAGTACTGGGGATCCGGGGGATCCGAACTCAGCTCCTCATGACTGCATAGCAAACATTTAACCAACTAAGCCATCTGTACAGCCCTGGAGGACACTACTCTGGGGACAGTGGCAGTCCTCACGAATGGGCAGAGGCCTTGCTCAGTCTCAGATCTGCTCTGTGGCCTCTGAGACCCTCAGTGTTTTCTTTCTGTCTGACACCTCTAATGCCCCCCACACACACCATACCCCGACTGGGGTCCACTGTGAGTGTACTGACATGGTTTAGACAGAAGCCCAGCACAGGGCCTGGCTGGGGGAGCCCTGAGCAGAGAAGACAGTCATTAGCTAGTGACTCTCACTGGGTTCCTTCACCCCTTCAG
Seq C2 exon
GCACCTGCGAAGCAGACTGCATGCGGAAGCGTGCCGAGCAGAGCCTGCAAGCCGCCATCAAGATTCTGCGCAAGTCCATTGGTCGGAACCAGTTCTATGTCCAGGTCTTGGGCACTGAGTACGAGGTGGCCCAGCGGCCAGCCAAAGCACTGGAGGGAACCGGGACTTGCGGCATAGGCCAAATACTACAGGACGGCAAGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016763:ENSMUST00000076060:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.362 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAACTGCCACGTGACTTTTG
R:
CACACTTGCCGTCCTGTAGTA
Band lengths:
342-2079
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