MmuINT0141263 @ mm10
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:95169988-95170491:+
Coord C1 exon
chr3:95169988-95170140
Coord A exon
chr3:95170141-95170317
Coord C2 exon
chr3:95170318-95170491
Length
177 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATC
5' ss Score
6.99
3' ss Seq
CCTGAAGCCTGTCGCTCCAGGGC
3' ss Score
2.97
Exon sequences
Seq C1 exon
GCCAGGGTCCTGTGCAGGTGTGGGTGCAGCTGCCTCGTTCTCCTCCTCTCAAGACCTACCTGATGATGTCCTGCTCTTCATCAAGGCACACCCGCTGCTGGATCCTGCTGTGCCACCCGCCACCCATCAACCGCTCCTCACTCTGACTAGCAG
Seq A exon
GTAATCACGCCTCCTGCCCTCGCCAAGCCCTTCTTTTTCTTGTGTGGTCCATGAGGCGAATCCCACTGGGGTGAGGGCCTATGAAGCAGTAGGATGGGAGGCAGGGCATCTCGGTGCTCCTGGGAGTGCTCAAGCTTCATTAGACAAGCTGTCCTCACCTGAAGCCTGTCGCTCCAG
Seq C2 exon
GGCCCTGCTGACCCAGGTAGCTGTGGACGGAATGGCTGGTCCCCACAGAAATACTACTGTCCTGTTTCTTGGCTCCAACGATGGGACAGTGCTGAAGGTGCTACCTCCAGGGGGTCAGTCTTTGGGCTCTGAGCCTATCGTCTTGGAAGAGATTGATGCCTACAGCCATGCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777:ENSMUST00000090823:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.058 A=NA C2=0.034
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.2=100)
A:
NA
C2:
PF0140314=Sema=FE(13.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTCGTTCTCCTCCTCTCAA
R:
GCTCAGAGCCCAAAGACTGAC
Band lengths:
256-433
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