MmuINT0141266 @ mm10
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:95171173-95171389:+
Coord C1 exon
chr3:95171173-95171250
Coord A exon
chr3:95171251-95171333
Coord C2 exon
chr3:95171334-95171389
Length
83 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
CTACCTCCTCTTCCTTCTAGGAC
3' ss Score
12.1
Exon sequences
Seq C1 exon
GAGCTGCCTGGCTTCTCTGGACCCATACTGTGGATGGCATCGATCCAGAGGCTGCATGAGTATCAGGGGACCTGGTGG
Seq A exon
GTAAGTGAGAAGCCCCTGGGCCTCCTGAGGAGAGTGCACAGCCAAGTGTAGGGCCATAGTGTGCTACCTCCTCTTCCTTCTAG
Seq C2 exon
GACTGATGTCGATCTGACTGGGAACCAGGAATCCACAGAGCACGGTGACTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777:ENSMUST00000090823:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.089 A=NA C2=0.940
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(41.9=100)
A:
NA
C2:
PF0143720=PSI=FE(30.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGCTTCTCTGGACCCATA
R:
CTTGGCAGTCACCGTGCTC
Band lengths:
128-211
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