RnoALTA0037826-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100421066-100421596:+
Coord C1 exon
chr9:100421066-100421179
Coord A exon
chr9:100421439-100421482
Coord C2 exon
chr9:100421483-100421596
Length
44 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TCCTCTCCTCCCTCCCCCAGAGT
3' ss Score
11.53
Exon sequences
Seq C1 exon
AGACAGACGAGTGCCAAGCACAGCCCTGCAGAAATGGAGGCTCCTGCAGGGACCTCCCCGGGGCTTTCATCTGCCAGTGCCCTGAAGGTTTTGTTGGAACCCACTGTGAAACAG
Seq A exon
AGTCCCTCCCTGCAGCTCGGGCCAACCCTTTGGGTGTTCTCCAG
Seq C2 exon
AGGTGGATGCCTGTGCCTCCAGCCCCTGCCAGCACGGAGGCCGGTGTGAGGACGGTGGTGGGGCCTACCTGTGCGTGTGTCCAGAGGGCTTCTTCGGCTACAACTGTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548-22-24,22-23-2/2
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
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
CCAGTGCCCTGAAGGTTTTGT
R:
GTTGTAGCCGAAGAAGCCCTC
Band lengths:
145-189
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]