MmuINT0139999 @ mm10
Intron Retention
Gene
ENSMUSG00000016763 | Scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:MGI Symbol;Acc:MGI:1890616]
Coordinates
chr15:83621029-83621531:-
Coord C1 exon
chr15:83621412-83621531
Coord A exon
chr15:83621134-83621411
Coord C2 exon
chr15:83621029-83621133
Length
278 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACC
5' ss Score
8.66
3' ss Seq
ACCCACTGGCCTCTCCACAGATT
3' ss Score
9.3
Exon sequences
Seq C1 exon
AGATGAACGGGTGCCTGTCTCGGTCCAAGGCCTCTGCCCAGGCCCAGCTGTCCTGTGGCAAGGTGGGTGGAGTGGAAAACTGCTTCCTGTCCTGCCTGGGCCACAGTCTCTTCATGCCAG
Seq A exon
GTAACCCCTGGCCCTCTGGGATGGGATGGGTTAACATGCTGCTTCCTGGGGTACACACCAGCCTCCCACTGCTCAGCAGGACAGAGCCCAGTGGAGAGCTCCCAGTCACAGGAGCAAGCGCTCCCAGACAGCTAGCTCCCTGGCTCTCTGTGGACCTGGGCCACTTCCCCAGGGGTCAGTCTTGATCTTCATTCGGGAGCCCCTTGGAGACCTCAGCAATCTGGGTCCCTAGAAGGGAGGTTCACCCTGGCTAACCTTACCCACTGGCCTCTCCACAG
Seq C2 exon
ATTCAGAAAGCAGCTACATCCTGAGCTGTGGTGTTCCAGGTCTCCAGGGCAAGACACTGCCAAAACGCAATGGCACTAGCTCCAGTACAGGGCCCGGCTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016763:ENSMUST00000076060:11
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=0.444
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:
AGATGAACGGGTGCCTGTCTC
R:
CAGCCGGGCCCTGTACTG
Band lengths:
220-498
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