BtaALTA0026521-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000016800 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:62871187-62871785:-
Coord C1 exon
chr10:62871708-62871785
Coord A exon
chr10:62871249-62871287
Coord C2 exon
chr10:62871187-62871248
Length
39 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
TCATTTGTGTTCCTATGAAGGCT
3' ss Score
7.13
Exon sequences
Seq C1 exon
GTCTTGTATTGCATCTCGAGACCCATACTGTGGCTGGTTAAGCCAAGGGGCCTGTGGTCGAGTGAGCCCAGCGATGCT
Seq A exon
GCTGTTAACTGAAGACTTGTTTGCTTTCCATAACCACAG
Seq C2 exon
CGCTGGAGGATTTGAACAAGACACAGAATATGGCAACACGGCCCATCTAGGGGACTGCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016800-21-17,21-16-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(41.9=100)
A:
NA
C2:
PF0143720=PSI=FE(33.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
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:
TTGCATCTCGAGACCCATACTG
R:
GCCGTGTTGCCATATTCTGTG
Band lengths:
112-151
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development