RnoALTA0009739-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148259335-148261482:+
Coord C1 exon
chr5:148259335-148259441
Coord A exon
chr5:148261390-148261407
Coord C2 exon
chr5:148261408-148261482
Length
18 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
TCCTGCGTTCCTAATGCTAGGGG
3' ss Score
7.17
Exon sequences
Seq C1 exon
GTGCTGAGGCTGTAGCTGATCTCTCTGGACCAACATGTTGGTATCCTGGGCTCCCGGCCTATGGGTGCTTGGGCTCTGGGCCACCTTCAGCCATGGAACAAATATAG
Seq A exon
GGGCCAACTCTGTCCCAG
Seq C2 exon
GTGAGCGCTGCCCAACTTCACAGGAAGAAGGACTCAAGCTGGAACACAGCAGTGACCCGTCAACCAACATGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475-4-3,4-2-2/2
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=0.577
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
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:
CATGTTGGTATCCTGGGCTCC
R:
TCTTCCTGTGAAGTTGGGCAG
Band lengths:
102-120
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]