MmuINT0140045 @ mm9
Intron Retention
Gene
ENSMUSG00000038677 | Scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:MGI Symbol;Acc:MGI:3045253]
Coordinates
chr17:28302372-28303093:+
Coord C1 exon
chr17:28302372-28302587
Coord A exon
chr17:28302588-28302931
Coord C2 exon
chr17:28302932-28303093
Length
344 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGG
5' ss Score
8.37
3' ss Seq
CGCGGCCGACTCTCCCTCAGTCA
3' ss Score
5.74
Exon sequences
Seq C1 exon
CTGGCTGTGGGCTGCCTTGCCTCCGACAGCGGATGGAACGGAGGCTGAAAGGGTCCCTGAAGATGCTCAGAAAGTCCATCAACCAAGACCGGTTCCTGCTGCGTCTGGCAGGCCTTGACTATGAGCTAGCCCACAAGCCAGGCCTGGGAGCTGGGGACCGAGCAGAGCTGGTGGAGGTCTGCCGACCTGGGCAGCACCGAGCAGGCACCAAGTGTG
Seq A exon
GTAAGGGAGCTTGCCGGGAAGCAAAGGTGTGGGGAGTGGGGGAGGCCCAACTTGGCCCTGGCTCAGAGCAGAACAGGACCCCTTGTCTCAGGTGAAGCTCTCAAAACGTGAGGTGGCGAAGCCCCTCCTGCCCACGGGCCTCCTTTCTCTGGTCCCAGGCTGAACCTCGGACACTAGGCAGGGCCGGCAGTTCTCCTGCACTCAGATTTGACATCCCTATCTCTCCAAGCAGGGTTCTGTTCGTTCCCTAATAGATCTCCCATGGCTGGAGGAGCGGGAAGGGGAGTCTTAGGCCTGGGTGGTGGGAGATGGGGGGGTGGCTAGCGCGGCCGACTCTCCCTCAG
Seq C2 exon
TCAGCTGCCCGCAGGGAACGTATTACCACGGCCAGACGGAGCAGTGTGTGCCATGCCCAGCGGGCACCTTCCAGGAGAGGGAAGGGCAGCTCTCCTGCGACCTTTGCCCTGGGAGTGATGCCCATGGGCCTCTTGGAGCCACCAACGTCACCACGTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038677-Scube3:NM_001004366:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=87.3)
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:
GACAGCGGATGGAACGGAG
R:
GTGGTGACGTTGGTGGCTC
Band lengths:
346-690
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: