MmuINT0141273 @ mm10
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:95168299-95168706:+
Coord C1 exon
chr3:95168299-95168389
Coord A exon
chr3:95168390-95168586
Coord C2 exon
chr3:95168587-95168706
Length
197 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
CACTCCCCTCATCTCTCCAGAGG
3' ss Score
7.4
Exon sequences
Seq C1 exon
ATAACATCTCTGCAACAGGAGGGTGAGGAGCTGAGTGGGCAGGCTCGATGCCCCTTTGATGCCACCCAGTCCACTGTGGCCATCTTTGCAG
Seq A exon
GTGTGCTCCTGGGCATGTAAGAGGCAGGCATGTGGCTGGAGGGAGTTCCTCTCCCACCTTGATCTCTCCCCAATGTCCTTGAGTGGAGGGTTGAGGTAGGGGCTGGGACCAGGCCTAGGTAGATATCTGTGTACACCAGTAGGAGACAAGCTGCAGATTCTGAGCTTTCTGTGACCCCACTCCCCTCATCTCTCCAG
Seq C2 exon
AGGGCAGTTTGTACTCAGCCACAGCAGCAGATTTCCAGGCCAGTGATGCTGTAGTTTACAGAAGTCTTGGACCTCAGCCTCCACTCCGTTCTGCAAAGTATGACTCCAAGTGGCTTCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777:ENSMUST00000090823:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.026 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(23.6=100),PF0140314=Sema=PU(1.1=9.7)
A:
NA
C2:
PF0140314=Sema=FE(9.6=100)
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:
TAACATCTCTGCAACAGGAGGG
R:
CTCGAAGCCACTTGGAGTCAT
Band lengths:
210-407
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