BtaALTA0028152-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120785461-120786000:+
Coord C1 exon
chr3:120785461-120785574
Coord A exon
chr3:120785844-120785886
Coord C2 exon
chr3:120785887-120786000
Length
43 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TCCTCTCCTCCCTCCCCCAGACA
3' ss Score
11.72
Exon sequences
Seq C1 exon
AGACAGACAAATGCCAGGCACAGCCCTGCAGAAACGGAGGCACCTGCAGGGACCTCCCGGGGGCCTCTGTCTGCCAGTGCCCCCCCGGTTTCACTGGAGTCCACTGCGAGACAG
Seq A exon
ACACCCCCTTGCTGCCCTGGCCGACTCTCTGGGTGTTCTCCAG
Seq C2 exon
AGGTGGATGCCTGCGACTCCAGCCCCTGCCAGCACGGAGGCCGCTGTGAGAACGGTGGCGGGGCCTACCTGTGCGTCTGCCCAGAGGGCTTCTTCGGCTACCACTGTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132-20-25,20-24-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
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=79.5)
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
(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:
CGGTTTCACTGGAGTCCACTG
R:
TGTCTCACAGTGGTAGCCGAA
Band lengths:
142-185
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development