MmuINT0140050 @ mm9
Intron Retention
Gene
ENSMUSG00000038677 | Scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:MGI Symbol;Acc:MGI:3045253]
Coordinates
chr17:28289343-28290629:+
Coord C1 exon
chr17:28289343-28289465
Coord A exon
chr17:28289466-28290503
Coord C2 exon
chr17:28290504-28290629
Length
1038 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGTTTTTTCTCTCTGCACAGACG
3' ss Score
10.23
Exon sequences
Seq C1 exon
ATGTAGATGAGTGTGTGGAAGGCACGGACAATTGCCACATCGATGCCATCTGCCAGAATACCCCACGGTCTTACAAGTGCATCTGCAAGTCCGGCTACACGGGGGACGGGAAGCACTGCAAAG
Seq A exon
GTGAGCCTGGGAGGTCTCCACTGCAAAGGTGAGCCTGGGAGGGTCCCCAGGATGGGAAGCACTGCAAAGGTGAGACTGGGAGGGTCCCCAGGATGGGAAGCACTGCAAAGGTGAGACTGGGAGGGTCCCTACTGCAAGGTGAGCCTGGGAGGTCTCCACTGCAAAGGTGAGCCTGGGAGGGTCCCCACTGCAAAGGTGAGACTGGGAGGTCCTCACTGCAAAGGTGAGACTGGGAGGGTCCCCAGGATGGGAAGCACTGCAAAGGTGAGACTGGGAGGGTCCCCACTGCAAGGTGAGCCTGGGAGGTCTCCACTGCAAAGGTGAGCCTGGGAGGGTCCCCACTGCAAAGATGAGACTGGGAGGTCCTCACAGCAAAGGTGAGACTGGGAGGGTCCCCAGGATGGGAAGCACTGCAAAGGTGAGACTGGGAGGTCCCCAGGAGGAGCTCGCAGGAGCCTCGGGGCCTGCACCATGGTTTCCAGGGGCCCACAACCTCCACAGGCCGAGGAGGACTGCCGCATCTTCCCAGAGATCGCACAGGGTTGGGGTGGACACCAAAGCATCACACAGCCAAGCTGTGCTGGTGGGGACACACTTCATAGCCTTCATAGCTCTCTGGGGCTGGCACACCTCAGTTACAAAACTAAGGCCCGAAGATCCCTGAGACAGGAGCCTGTACTGGCGCCTGTCATAGCATGCGCAAAGGACCAGACCTGTGAACCCCAGTGGGAGTTCACCCACAAGCAAGCACATCACTTGCTATAAAAACACTGCAGAGTGGCTGGGAATAGCATTCTCAGGGACAAAGTACACGTTACTTTCTGTTGACATAATACACTGAGAACTACAGTAGCCTCCTGGGACCCAGGGAATGGGGGTGTTGGTTCAAGGATGACAGTCCTTCCCAGTAATACCACAACTAAAGAACGTTCGAGAACTTTATATGAATGATGTAATCAAAAGCATGAAATTAAAAATGGCATAGCTGTTTGCCTGTGACCGTCAACATCTTCCGGTGTGTTTTTTCTCTCTGCACAG
Seq C2 exon
ACGTGGATGAGTGTGAACGGGAGGACAACGCAGGCTGTGTGCACGACTGTGTCAACATCCCTGGTAATTACCGGTGTACCTGCTACGACGGATTTCACCTGGCACATGACGGACACAACTGTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038677-Scube3:NM_001004366:2
Average complexity
IR-C
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:
PF129472=EGF_3=WD(100=85.7)
A:
NA
C2:
PF126622=cEGF=PU(83.3=46.5)
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:
ATGTAGATGAGTGTGTGGAAGGC
R:
GACAGTTGTGTCCGTCATGTG
Band lengths:
246-1284
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: