MmuINT0140055 @ mm10
Intron Retention
Gene
ENSMUSG00000038677 | Scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:MGI Symbol;Acc:MGI:3045253]
Coordinates
chr17:28156762-28157189:+
Coord C1 exon
chr17:28156762-28156887
Coord A exon
chr17:28156888-28157072
Coord C2 exon
chr17:28157073-28157189
Length
185 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGA
5' ss Score
3.37
3' ss Seq
CATGTCTCCTCTCTGTGCAGTGA
3' ss Score
9.76
Exon sequences
Seq C1 exon
AAGGAATGAACTGCATGAACAAGAACCACGGCTGTGCCCACATTTGCCGGGAGACTCCCAAGGGGGGCATTGCCTGTGAATGCCGCCCTGGCTTCGAGCTCACCAAGAACCAACGGGACTGTAAAT
Seq A exon
GTGAGATTTGTGAGGGCAGGAGAATGGGGGGGACAGGAAGGTGTGGGGCCTCAGTAGCCAGAGGGCAGGGATGAGATGAAAGAGGCCTGGGGGCGGGGCACAGTGAGGAAAAGGGGCAGCTTTCCCCACCTTGAAGACCTGCAGCACAAGGGACAAGCAGGCTGACATGTCTCCTCTCTGTGCAG
Seq C2 exon
TGACCTGCAACTATGGTAATGGCGGCTGCCAGCACACCTGCGATGACACGGAGCAGGGTCCTCGGTGCGGCTGCCACGTCAAGTTTGTGCTCCACACCGACGGGAAGACATGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038677:ENSMUST00000043503:5
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=0.000
Domain overlap (PFAM):
C1:
PF146701=FXa_inhibition=WD(100=86.0)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=90.0)
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:
AGGAATGAACTGCATGAACAAGA
R:
CAATGCATGTCTTCCCGTCGG
Band lengths:
242-427
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