BtaALTA0028154-3/3 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120768084-120769531:+
Coord C1 exon
chr3:120768084-120768197
Coord A exon
chr3:120769418-120769439
Coord C2 exon
chr3:120769440-120769531
Length
22 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CGTGCACACTGCGCTCACAGCAG
3' ss Score
4.61
Exon sequences
Seq C1 exon
ATGTGAACGAGTGCGCTTCCCACCCGTGTCAGAACGGTGGGACCTGCACACACGGCGTCAACAGCTTCAGCTGCCAGTGCCCTGCCGGCTTCAGGGGACCCACCTGCGAGACAG
Seq A exon
CAGAGTCTCCGTGCGATGACAG
Seq C2 exon
AGAGTGTCAGAACGGCGGCTGGTGCCGGGCGGAGGGCGGCGCCGCGGCGTGCGTGTGCCCAGCCGGCTACACAGGGGCGGCCTGCGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132-8-7,8-6,8-5-3/3
Average complexity
Alt3
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:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0000822=EGF=WD(100=76.9)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
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:
CTTCCCACCCGTGTCAGAAC
R:
GCCGCCGTTCTGACACTC
Band lengths:
118-140
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development