MmuALTD0012583-2/2 @ 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
chr3:94972509-94972819:+
Coord C1 exon
chr3:94972509-94972605
Coord A exon
chr3:94972606-94972628
Coord C2 exon
chr3:94972731-94972819
Length
23 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
3' ss Seq
TTCCTGTCACTTTGCCTCAGAGC
3' ss Score
8.1
Exon sequences
Seq C1 exon
AGGGCAGTTTGTACTCAGCCACAGCAGCAGATTTCCAGGCCAGTGATGCTGTAGTTTACAGAAGTCTTGGACCTCAGCCTCCACTCCGTTCTGCAAA
Seq A exon
GTATGACTCCAAGTGGCTTCGAG
Seq C2 exon
AGCCACACTTTGTCTATGCGTTGGAGCATGGAGAGCACGTCTACTTCTTCTTCCGAGAAGTCTCTGTGGAGGATGCCCGCTTAGGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777-20-14,21-14-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.0=100)
A:
NA
C2:
PF0140314=Sema=PD(5.5=23.3),PF0140314=Sema=FE(11.1=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTCCAGGCCAGTGATGCTG
R:
AGTAGACGTGCTCTCCATGCT
Band lengths:
112-135
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: