BtaALTD0019409-2/2 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000007281 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr3:19722929-19723316:+
Coord C1 exon
chr3:19722929-19723025
Coord A exon
chr3:19723026-19723048
Coord C2 exon
chr3:19723228-19723316
Length
23 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGG
5' ss Score
4.94
3' ss Seq
TCCTGTCACTTCCCACTCAGAGC
3' ss Score
7.25
Exon sequences
Seq C1 exon
AGGGCAGCCTGTACTCAGCCACAGCTGCAGACTTCCAGGCCAGTGATGCTGTGGTTTACCGAAGCCTTGGGCCTCAGCCCCCGCTCCGCTCCGCCAA
Seq A exon
GTACGACTCCAAGTGGCTCCGAG
Seq C2 exon
AGCCACACTTTGTCCACGCTTTGGAGCACGGAGACCATGTCTACTTCTTCTTCCGAGAAGTCTCTGTGGAGGATGCCCGGCTGGGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007281-15-12,16-12-2/2
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(9.4=100)
A:
NA
C2:
PF0140314=Sema=FE(6.8=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCAGTGATGCTGTGGTTTA
R:
TAGACATGGTCTCCGTGCTCC
Band lengths:
103-126
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development