MmuINT0140048 @ mm9
Intron Retention
Gene
ENSMUSG00000038677 | Scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:MGI Symbol;Acc:MGI:3045253]
Coordinates
chr17:28303971-28304652:+
Coord C1 exon
chr17:28303971-28304132
Coord A exon
chr17:28304133-28304454
Coord C2 exon
chr17:28304455-28304652
Length
322 bp
Sequences
Splice sites
5' ss Seq
AGAGTACGT
5' ss Score
6.58
3' ss Seq
CCACCGGGGTGTGGCTGCAGATC
3' ss Score
5.29
Exon sequences
Seq C1 exon
TCCAGTGCTCCCCGGGCCACTACTATAACACTAGCATCCATCGCTGTATCCGCTGTGCTGTGGGCTCCTACCAGCCAGATTTCCGTCAGAACTTCTGCACCCGCTGCCCAGGAAATACAAGCACTGACTTTGATGGCTCGACCAGTGTGGCCCAGTGCAAGA
Seq A exon
GTACGTGGCTGGCCAGGCTGTAGGGAGTGGAAAGAGATCTTGGAGCCATGTGCACGGGAAAAGGGGGTGGGAGGTGGTAAGGCAGCGGGGAAGGGGGCCGGAGTGGGTGGGTGGGCAGCTGTCAGGGATGCCTGTAGCATCCTTTTGGATACTGGAAGGGCAGGAGGAGGGTGGACCCAGCACCCCGGAAGAGCAGGTGGTGATCTAGCATGGTTCACCACCTATGTTTGTTCTCCCCCTTCAAGCCCCTCAGCCTGCCCACCACGGTTCCCCACTGACTGTCCATCTCTCCCTTGCTCTCTCCACCGGGGTGTGGCTGCAG
Seq C2 exon
ATCGGCAGTGTGGCGGGGAGCTAGGTGAGTTCACTGGCTACATCGAGTCTCCCAACTACCCGGGCAACTACCCGGCCGGTGTGGAGTGCGTCTGGAACATCAACCCCCCACCCAAGCGCAAGATCCTCATCGTGGTCCCCGAGATCTTCCTGCCCTCCGAGGATGAGTGTGGGGACGTCCTGGTCATGAGAAAGAACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038677-Scube3:NM_001004366:18
Average complexity
IR-S
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:
PF076998=GCC2_GCC3=WD(100=87.3)
A:
NA
C2:
PF0043115=CUB=PU(57.3=94.0)
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:
CCCCGGGCCACTACTATAACA
R:
TTCTCATGACCAGGACGTCCC
Band lengths:
345-667
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: