MmuINT0140004 @ mm9
Intron Retention
Gene
ENSMUSG00000016763 | Scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:MGI Symbol;Acc:MGI:1890616]
Coordinates
chr15:83443868-83445461:-
Coord C1 exon
chr15:83445300-83445461
Coord A exon
chr15:83444036-83445299
Coord C2 exon
chr15:83443868-83444035
Length
1264 bp
Sequences
Splice sites
5' ss Seq
GAGGCGAGT
5' ss Score
2.28
3' ss Seq
CCGTGACTTCTGACTTCCAGGCC
3' ss Score
7.38
Exon sequences
Seq C1 exon
TACCGTGTGCTCCTGGCACCTACTTCAGTGGTGACCCAGGCCAGTGTATGCCATGCGTGTCGGGAACCTACCAGGACATGGAAGGCCAGCTCAGCTGCACGCCATGCCCCAGCAGCGAAGGACTGGGTCTGGCTGGTGCCCGAAACGTATCCGAATGTGGAG
Seq A exon
GCGAGTGTGGCCCACCTGGAGGGAGGGGGTCAGGTGGGGACAAGTTCCCAACAGGGCCCATCAGCCCCTCACAAGGCTCCCTGAGCCAAAGCATGTGCAGTTATAAACGGTGGCCTTGTCGGAAGCTCTACCCTTTCCAAAGACTTAGTGTCCACATAGTCACCATGCACAGAAAGGCCTTACAGCATGTCCATACAACCACTGACAGACTGAGGTGTGGCTTGTCACAGAAAACATGGGTGCTTAAAAGACACTCCACGTTCTGAGCGATGCTCCACCCAAGTCAAGAGATCGACTTTAGCCAGAGCTTTCTCCACATACAGCATGCTGTTTGCCTTGTTGGTGGATGAGATGCCAGTTTTCAATTTAATAGCAGGGGCAGTTGTATTATCACCCAGCCCTGCCATGGACAGCCCACTCAGCCCCTTGAGCAACATGACTCAGAGTTCCCCACTGGACTCTCCCACTGGGCCATACTGGGCTCACTCTAGAGAACGCACACCAAGGGCTTGACCCTGGAAAGGGATAGTGTCCAGGAGGGTGGGTGAGGAGCAGAGACCTCCAAGCCTTCTCCAAGGCACACGAGAGCCCACCTAGAGACCAACCAGAGGTCCTGTGGGTGCCAGCTACTCCCTGATCCTCTAGCCCCCAGGAATGGGATTCCCAGGACAATGGCAGCCATAAAGCACAGGGTAGCCATGGGAGGGGACAGTCTCCACTTGGATGGAAGCTAAGAATCTCAGAGACGGGGTCAAGAGGACATTGCACCCACTCCATATTGGAACACCTGCACCCACATTTCTGTGGAAGTGTTGAGCTCAGGGTGGCTTTCCTGTGGTCCCTTTTTGTCCCAGCCAGGCCCTTGGTTCTCAAAGACCCTCCCTTCCCTCCTCCCCCTCTTCTGGCCTGTCCAGCTGACAGATCAGATGGCATCAGCCTAGAACCCTAGGCTATTCCTTCTGTGAGCACCTGAGACCTGCCCCTGGGAAGCTGGGATGTAAACACCCCCTCCTCTGTACCCCAGCTTGACAGTGAGGCCCCCTTGCTCCTTACTTAGCCCCAGCCATTGCTGCTGCTGAGAGATGGGAGGGCAGTCTGGCAAAGCCATACAGTAGACAACTGTCAGCCTCAAGATCCAGGGCCTGCAAACTCCAATCTAAGTTGCCCAGGGTACCTTTACCAGGAAGGGCAGGGCCAACCTCTCAAATCTTAGTAGCCACTGCAGCACCTCTCCCCTACCTGAGCCGTGACTTCTGACTTCCAG
Seq C2 exon
GCCAGTGCTCTCCAGGCTACTTCTCAGCGGATGGGTTCAAGCCTTGCCAGGCCTGCCCTGTGGGCACATACCAGCCCGAGCCTGGGCGAACCGGCTGCTTCCCCTGTGGAGGCGGGCTGCTCACCAAACACACGGGTACCGCCTCTTTCCAGGACTGCGAGGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016763-Scube1:NM_022723:16
Average complexity
IR-S
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:
PF076998=GCC2_GCC3=WD(100=87.3)
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=84.2)
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:
CTGGCACCTACTTCAGTGGTG
R:
CTTTGGCCTCGCAGTCCTG
Band lengths:
318-1582
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: