MmuINT0141268 @ mm10
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:95171558-95171886:+
Coord C1 exon
chr3:95171558-95171602
Coord A exon
chr3:95171603-95171790
Coord C2 exon
chr3:95171791-95171886
Length
188 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
GACCTGGTCTCTGTTACCAGTGC
3' ss Score
7.16
Exon sequences
Seq C1 exon
ATGGAGCGACCGGGAGTCAGTCTGGCCCTGGAGATTCTGCTTATG
Seq A exon
GTGAGTTCTGGCCTCAGTGTCCTGTTCCCTTTCTTGGCCTACACAACCAAATCCATTTGGGCTATAAGCAGACCTTGAACAGTCAGATGAGACTCTGGAATTGTGGACTCCTGGGTTCCAAAGGGGGTGGGGGGGCTCTTGGTGGAGAGCATACGTCTCACTGGCTCTGACCTGGTCTCTGTTACCAG
Seq C2 exon
TGCTTCTGGGTCCTGGCCCTTCCCCTGAGACCCCCAGTTCCCCCAGTGATGCCCAACAAGGGCCCCAGTCTTCCACTCTTGGAGCTCACACACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777:ENSMUST00000090823:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.887 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(11.3=43.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCGACCGGGAGTCAGTC
R:
CCTGTGTGTGAGCTCCAAGAG
Band lengths:
138-326
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