MmuALTD0012582-2/2 @ mm9
Alternative 5'ss
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:94971546-94972022:+
Coord C1 exon
chr3:94971546-94971602
Coord A exon
chr3:94971603-94971648
Coord C2 exon
chr3:94971921-94972022
Length
46 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTG
5' ss Score
6.13
3' ss Seq
TAGAATTTTGGGTTCTCTAGGAC
3' ss Score
6.8
Exon sequences
Seq C1 exon
TTTCTGACATGGAGGAGTCAAGATATGGAGAACTGTGCAGTCCGGGGAAAGCTGACG
Seq A exon
GTGAGGAGTGGAGTGTAATTGGAGGGAAGGCGAGGACTGCCTTCAG
Seq C2 exon
GACGAATGCTACAACTACATCCGTGTTCTTGTTCCCTGGAACTCGCAGACACTTCTTGCCTGTGGAACAAATTCCTTCAGCCCTATGTGCCGCAGCTATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777-15-10,16-10-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(14.2=100)
A:
NA
C2:
PF0140314=Sema=PU(1.5=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
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:
TATGGAGAACTGTGCAGTCCG
R:
CATAGCTGCGGCACATAGGG
Band lengths:
134-180
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: