BtaALTA0028154-2/3 @ 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
chr3:120769421-120769439
Coord C2 exon
chr3:120769440-120769531
Length
19 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
GCACACTGCGCTCACAGCAGAGT
3' ss Score
1.47
Exon sequences
Seq C1 exon
ATGTGAACGAGTGCGCTTCCCACCCGTGTCAGAACGGTGGGACCTGCACACACGGCGTCAACAGCTTCAGCTGCCAGTGCCCTGCCGGCTTCAGGGGACCCACCTGCGAGACAG
Seq A exon
AGTCTCCGTGCGATGACAG
Seq C2 exon
AGAGTGTCAGAACGGCGGCTGGTGCCGGGCGGAGGGCGGCGCCGCGGCGTGCGTGTGCCCAGCCGGCTACACAGGGGCGGCCTGCGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132-8-7,8-6,8-5-2/3
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:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0000822=EGF=WD(100=76.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
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:
118-137
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development