BtaALTA0028153-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120786789-120787383:+
Coord C1 exon
chr3:120786789-120786902
Coord A exon
chr3:120787087-120787112
Coord C2 exon
chr3:120787113-120787383
Length
26 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TCTTGACCGAAACCCTGAAGAGC
3' ss Score
-1.74
Exon sequences
Seq C1 exon
TGAGTGACCCCTGCTTCTCCAGCCCCTGTGGAGGCCGCGGCTACTGCCTGGCCAGCAACGGGTCCCACAGCTGCACCTGTAAAGTGGGCTACACCGGCAGGGACTGTGACAAAG
Seq A exon
AGCTCTTCCCACCAACGGCCCTCAAG
Seq C2 exon
GTGGAGCAAGTGGAAGAGAGTGGGGTCTCCATCTCCTGGCGCCCCCCCGAAGGCCCAGCGGCCAGGCAGCTGCTGGATGGCTATGCCGTCACCTACGTGTCCTCGGACGGCTCCTACCGCCGCACAGACTTCGTGGACCGGGGCCGCTCCGCGCACCAGCTCCGGGCCCTGGCACCCGGCAGGGCCTACAACGTCTCTGTCTTCTCGGTCAAGCGCAACGCCAACAACAAGAACGACATCAGCAGGCCCGTGGTGCTGCTTGCCCGCACGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132-22-28,22-27-2/2
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=0.070
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0004116=fn3=WD(100=83.0)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCTGTAAAGTGGGCTACA
R:
CATAGCCATCCAGCAGCTGC
Band lengths:
127-153
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development