MmuINT0141263 @ mm9
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:94973910-94974413:+
Coord C1 exon
chr3:94973910-94974062
Coord A exon
chr3:94974063-94974239
Coord C2 exon
chr3:94974240-94974413
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-Sema6c:NM_011351:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.058 A=NA C2=0.038
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: