MmuINT0140047 @ mm10
Intron Retention
Gene
ENSMUSG00000038677 | Scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:MGI Symbol;Acc:MGI:3045253]
Coordinates
chr17:28166357-28167187:+
Coord C1 exon
chr17:28166357-28166524
Coord A exon
chr17:28166525-28167025
Coord C2 exon
chr17:28167026-28167187
Length
501 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CCCTCTTCTCTCGCCTGCAGTCC
3' ss Score
11.54
Exon sequences
Seq C1 exon
GTCAGTGCCCACCTGGCCACCATTCAGGAGATGGGTTTAAGCCCTGCCAGCCATGCCCCCGGGGCACCTATCAGCCTGAAGCAGGGCGAACCCTGTGCTTCCCCTGTGGCGGAGGCCTCACCACCAAGCATGAGGGGGCAGTCTCCTTCCAGGACTGCGACACCAAAG
Seq A exon
GTGAGCAGGTTATTTACTCCCCGGAGCTTCCTATCCTCAGCTGCCACCCACCCCACACATCTCCAAGCCCCTCCACAGACCTGAGTGTTATCTGACCATCTTCCCTCAAAAGTGAAGACCCAGGTACCTAACTGTACATGTTCTTGTTTCAGAGCTGCCCCTTGGGCCAGACCTGGGGATAGAAAGTGACTAAACCCTTCCTCCCTGTCCAGAGTACATTGCAGATTGGTAGCCATTTCCCTCCATCCCCCTAAGTGAGCTCCTGTATCAGTCTGACACTGCTCAGGGAGGGCCTGCAGGAAGAGGAGGGTGCTGTAGCCAGCCACTTTGGAAGGTCTCTCTTCCCTGGCTTTAGACTATGTCTGGGAAAGGTAGGGACCCTGGAAGAAACCTGGGAGTCTCTGATGTCTGGATTCTCCATGACAGATGTGCCTGTCTATCCACGGTCCAGATGCCCACTTTCCTACCATCTTAGCTTCTGCCCTCTTCTCTCGCCTGCAG
Seq C2 exon
TCCAGTGCTCCCCGGGCCACTACTATAACACTAGCATCCATCGCTGTATCCGCTGTGCTGTGGGCTCCTACCAGCCAGATTTCCGTCAGAACTTCTGCACCCGCTGCCCAGGAAATACAAGCACTGACTTTGATGGCTCGACCAGTGTGGCCCAGTGCAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038677:ENSMUST00000043503:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.009 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF076998=GCC2_GCC3=WD(100=84.2)
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:
CTGGCCACCATTCAGGAGATG
R:
TCTTGCACTGGGCCACACT
Band lengths:
318-819
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