BtaALTD0020545-1/3 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120765390-120767864:+
Coord C1 exon
chr3:120765390-120765524
Coord A exon
NA
Coord C2 exon
chr3:120767739-120767864
Length
0 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGC
5' ss Score
9.1
3' ss Seq
TGCCCTCCATGTGTCCGCAGCCT
3' ss Score
10.31
Exon sequences
Seq C1 exon
GCCGGCTTCAACGCGGGAGACGGGCAGCGCTACTTCAGCATCCCCGGCTCGCGCACAGCGGACATGGCGGAGGTGGAGACCACCACCAACGTGGGCGTGCCCGGGCGCTGGGCGTTCAGAATCGATGATGCCCAG
Seq A exon
NA
Seq C2 exon
CCTCCGTGTGCCAGACACTGCGTCCCTGCCTCAACGGCGGCAAGTGCATTGACGACTGCGTCACGGGCAACCCCTCCTATACCTGCTCCTGCCTCTCAGGCTTCACGGGGAGGACGTGCCACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132-4-3,5-3,6-3-1/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence exclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.073 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF061199=NIDO=PD(47.3=78.2)
A:
NA
C2:
PF0000822=EGF=WD(100=83.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
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:
CTGGGCGTTCAGAATCGATGA
R:
CTGAGAGGCAGGAGCAGGTAT
Band lengths:
127-155
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development