MmuINT0140017 @ mm10
Intron Retention
Gene
ENSMUSG00000016763 | Scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:MGI Symbol;Acc:MGI:1890616]
Coordinates
chr15:83627952-83629500:-
Coord C1 exon
chr15:83629384-83629500
Coord A exon
chr15:83628075-83629383
Coord C2 exon
chr15:83627952-83628074
Length
1309 bp
Sequences
Splice sites
5' ss Seq
GAGGTCTGC
5' ss Score
3.9
3' ss Seq
ACTCCTGCCTGTGTTTCCAGACG
3' ss Score
8.82
Exon sequences
Seq C1 exon
ACATTGACGAGTGTTCCTTTGAGCGGACCTGTGACCACATCTGCATCAACTCCCCCGGCAGTTTCCAGTGCCTGTGCCGCCGAGGCTACACACTCTACGGGACAACCCACTGCGGAG
Seq A exon
GTCTGCAGCCCGCCCGCCAGGGCCACCTCCCCCTCGAGGCACGCGCCTGGCATATGGCCATCAACAGTGCTCCCCACACCCCAATCGTGACTTTGACCCTGGTGGGCCTGGGAGGGACCTTGCAAGGCTGGGATTCTGCCAAACAGGCACAAGGTAGTGGACAGGGGTTGGGGGGAGACAGGGCATGGGAGGCACCATGAGGGTGCCTTAGCAGGTTTGGAAACATAAACCCAGAACCTCATTTCCTGGGGTAACCAGTCCAGAAGTGGGTGGCCAATGCACAGAAATTTCCAGAAAGTACATTCTAGAGACAATGAGAATCCTAAAGGAGGAACCTTTGGGTCAAGACGGGAAAGCAGTTCGGGGGAACAGCATATACAGACGCACAGAGGCAAGGATGTAGCAGGGATGAGCCCATGAGCAGCAGGAAACAGGGTAATATCCCCCGGGGAGATACATGCCCAGGATGTACAGAGCTGTGTGAGCCCAGAGGGAGCCTTGAGGGTAGCCTGAGGGCTTCTTTACAGTGCTACACACCAACGCAGGAAGCCTTGAAGCAGAGTGCTAGATAGTCATATCTGTATGACAAAGGACTCTGGCTGTTGGAGGAAGGGAACATGGGATCCAGGCAGCCCATGGGGGAGATGGCTCATGGCCTGAGACCTTATCCTCTGGGTTGGGAGGAGGGGTAGGGCAGAGCTGGAGAGAAGATTCAAGAGCCTGGGATGGAGGAATTCTTACCTAGAGCCCCGGGTTCCACAGCCAGCACCACAGTGAACAAGAGCTTGGACTGAGCCAGAGGACATTAGGCCAGATGTGGCTGGTGAAGATGGGAAGAGAGGGGGTCATCGTGGCCTCTCTTCTTTCTCTGTGACCTGAGAACAGTGCAAAGCTAGAGAGGGCCAGGTCATACTGGAGACAGGGGCGGAATAGCCACTTGATGCTAGTGCCATTGTCAAGGGACTCTCAAATGCCGTTTCCCTGACTGATAGGATAGCATACATGTGTGCTGGCATCCAGGGCGGCCTGGAGCAGGAAGAGCTAGCTAGCCCTTGCCTAAAGGAGGTTTTTGGTCAGAGGAGGAAGAGTCTCCAGTGACTTCTTTCAGACTGGTGCCCACTATCCAGGAGGGGAAACTAAGGCTGTCGAGGAGCCAAAGCTTTCCCTGGGGGGATGAGATATCCGTGATGCCCAAGACCTCTGCCAGACCGGACCAGAATCAGGAGCTTCCTGGTCTCTGGTCCTGGGTGTGTGACCTGGGCTGCTATTTCCCACCCCCTCCGGCCCTCACTCCTGCCTGTGTTTCCAG
Seq C2 exon
ACGTGGATGAATGTAGCATGAACAACGGCAGCTGTGAGCAGGGCTGTGTCAACACCAAGGGCAGCTACGAGTGTGTGTGCCCACCAGGGAGGAGGCTGCACTGGAATCAGAAGGACTGTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016763:ENSMUST00000076060:9
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:
PF0764510=EGF_CA=WD(100=95.0)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=85.7)
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:
CATTGACGAGTGTTCCTTTGAGC
R:
CCACACAGTCCTTCTGATTCCA
Band lengths:
239-1548
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