HsaALTD0005768-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000143434 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:10740]
Coordinates
chr1:151110187-151110581:-
Coord C1 exon
chr1:151110485-151110581
Coord A exon
chr1:151110462-151110484
Coord C2 exon
chr1:151110187-151110275
Length
23 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGG
5' ss Score
4.94
3' ss Seq
CCTGTCATTCCCCATCTTAGAGC
3' ss Score
8.16
Exon sequences
Seq C1 exon
AGGGCAGCCTGTACTCAGCCACAGCTGCGGATTTCCAGGCCAGTGATGCTGTAGTTTACAGAAGCCTTGGGCCCCAGCCCCCACTCCGCTCCGCCAA
Seq A exon
GTATGACTCCAAGTGGCTCCGAG
Seq C2 exon
AGCCACACTTTGTCCAGGCCTTGGAGCATGGAGACCATGTCTACTTCTTCTTCCGCGAGGTCTCTGTGGAGGATGCTCGGCTGGGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434-13-12,14-12-2/2
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(9.5=100)
A:
NA
C2:
PF0140314=Sema=PD(0.1=0.0),PF0140314=Sema=FE(10.9=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTCCAGGCCAGTGATGCTG
R:
ATGGTCTCCATGCTCCAAGGC
Band lengths:
105-128
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)