MmuINT0140007 @ mm10
Intron Retention
Gene
ENSMUSG00000016763 | Scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:MGI Symbol;Acc:MGI:1890616]
Coordinates
chr15:83608724-83610351:-
Coord C1 exon
chr15:83610154-83610351
Coord A exon
chr15:83608877-83610153
Coord C2 exon
chr15:83608724-83608876
Length
1277 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGT
5' ss Score
7.64
3' ss Seq
AAAAGCCTGCATCCCTACAGCCT
3' ss Score
4.29
Exon sequences
Seq C1 exon
ACCAGCACTGCGGCGGCGAACTTGGTGACTACACAGGCTACATCGAGTCCCCCAACTACCCTGGCGACTACCCAGCCAATGCAGAGTGTGTGTGGCACATCGCACCTCCCCCAAAGCGCAGGATCCTAATCGTAGTCCCGGAGATCTTCCTACCCATCGAGGACGAGTGTGGTGATGTCCTGGTCATGAGAAAGAGTG
Seq A exon
GTATGTTCCTGGGCTGGGGCTGGGACAGTAAGAGCAAGACAGCTCATGTGCTCAGAAAGTGGGTGACTCCGAAGTCCCCACGAGGTAGGATAGAAGTTCACCTGAGCCAGGTGTAAGAGCTGAAACATACAGAACTCTAGGGAAAGGTCATGAAGGCTTAGGGCTACCCTGAGATAGGAATCTGGGTCTAGTCAATTGTGGTCTCAACTTATCAGCCAGTCTCTTCCAGTGTCTAGCCAGCTACAGTGTTCCCTCGGAGGCTTGCAGGAACCAAGGGCCATCCAGATACACATAGTCGCCTGGGCTAGCCCTTCCTAGAGCCTTAGCTATGCACCCTGTCAGGTGAGGGAAGGATAGGGTGGGATAAACAGAGAGCCAGCCTTCAGCAGGGGTGGAAAAGGGTGCAGGCCACGATGGTGACAAACCCAGGAAGGAACTGAATGCCTGCACGGTCTTGGCCCTATCCTCAGCATCCTGACCAGAGACTTTACTTCACTGGGGGGTGGTCACCCATAGGAGTGAACTGTGAGCCAGAATATTAAGGGAGAAGGCTAGAGACCCAAACAGGCACAAAACTACATAGTTGGTCTAGAGCTAGACCATCTGTGCATAGGAAGACAGGTGGCAAGCAAAGGAGGTGGCTCAGCCAAAGTTCTTGTGTGGCTCTGTGGCCTCGTGCATATATTACTTATTGGTTGGCTGACAGGCCAGAAAGCCACAGTGTACAGATGGAGGGTTACAGCCAGAAGGAATGAGGGCCCTGCCCAGCTGGTCAGAGCCTGGCCTTGGACCCCCTCCTGCATCCACTCTCATCACTAGCTCATGGACTACCCACAGGCAACACCCTTGTGAGGGTCAGGGAGGCAGCTCTGAGTTTACCCTTGTCACTCAGCCCCAGATGAGTCGACTTTCTACACCTGAGTTTCTGGTGGCTTTTGGTCCATGCTGACTCATCTCCTATACCTGCCTGAGCTGGTCTCCTTGTCCCTGTCATGGAGAAGGAGCCATGAGCCTGGGGGGAGACAGAGAGACCGTAAAGGGGAGTTCAACAGAGTAACAGGAATAAGGCTGGATGCAAGAGGCAGCAGGGAGGCTTCACGGGCAGGCAGTGGAAACAGGCCTCAGAAGGTTGGGGCAGCAGGCCAAGGGCAGAGCCAGAGAGGACCAAAGGAGCTGGGTGTTCTGATGCAGGAGGCTGATGAGGTGGGGGAGGTGAGCGGCCTAAGGTACTGAGCTGTAGACCTGGGGCAGTGTTGCAAAAGCCTGCATCCCTACAG
Seq C2 exon
CCTCGCCCACGTCAGTCACCACCTATGAGACGTGCCAGACCTATGAGCGGCCCATCGCCTTTACCTCCCGTTCCCGCAAACTCTGGATCCAGTTCAAATCCAACGAAGCCAACAGTGGCAAAGGGTTTCAAGTGCCCTATGTCACCTATGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016763:ENSMUST00000076060:19
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:
PF0043115=CUB=PU(57.3=94.0)
A:
NA
C2:
PF0043115=CUB=PD(41.8=88.5)
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:
CGGCGAACTTGGTGACTACAC
R:
TCATAGGTGACATAGGGCACT
Band lengths:
336-1613
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