MmuINT0140050 @ mm10
Intron Retention
Gene
ENSMUSG00000038677 | Scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:MGI Symbol;Acc:MGI:3045253]
Coordinates
chr17:28152398-28153684:+
Coord C1 exon
chr17:28152398-28152520
Coord A exon
chr17:28152521-28153558
Coord C2 exon
chr17:28153559-28153684
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:ENSMUST00000043503:2
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:
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
- 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