BtaALTD0020545-2/3 @ 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
chr3:120765525-120765552
Coord C2 exon
chr3:120767739-120767864
Length
28 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
TGCCCTCCATGTGTCCGCAGCCT
3' ss Score
10.31
Exon sequences
Seq C1 exon
GCCGGCTTCAACGCGGGAGACGGGCAGCGCTACTTCAGCATCCCCGGCTCGCGCACAGCGGACATGGCGGAGGTGGAGACCACCACCAACGTGGGCGTGCCCGGGCGCTGGGCGTTCAGAATCGATGATGCCCAG
Seq A exon
GTGCGCGTGGGGGGCTGCGGCCATACAA
Seq C2 exon
CCTCCGTGTGCCAGACACTGCGTCCCTGCCTCAACGGCGGCAAGTGCATTGACGACTGCGTCACGGGCAACCCCTCCTATACCTGCTCCTGCCTCTCAGGCTTCACGGGGAGGACGTGCCACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132-4-3,5-3,6-3-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.073 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 Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
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