RnoALTA0009769-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176508585-176509019:+
Coord C1 exon
chr3:176508585-176508733
Coord A exon
chr3:176508890-176508902
Coord C2 exon
chr3:176508903-176509019
Length
13 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGC
5' ss Score
9.1
3' ss Seq
TCCTCCTCCTCCTCCCACAGATC
3' ss Score
12.85
Exon sequences
Seq C1 exon
CTGCAGCAAACAGGAGCCCCCCATCCAGCCTGGCCTTGTCCTCGGAGACCCCCAACAGCCTGCAGGTCAGCTGGGCACCACCAAGTGGCCATGTCCTCCATTACCGGCTCAACTACACACTGGCCTCAGGCTCTGGACCAGAGAAATCG
Seq A exon
ATCTCTGTACCAG
Seq C2 exon
GCACCAGGAGCCATGTTGTACTTCGTGATCTGATGTCTGCCGCCAAGTACAGGGTCCTGGTCTCAGCTGTCTATGGAGCAGGGGAGAGCATGGCAGTGTCTGCCACATACCGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326-22-26,22-25-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.230 A=NA C2=0.034
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(54.3=88.0)
A:
NA
C2:
PF0004116=fn3=PD(43.2=79.5)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
GCTCAACTACACACTGGCCTC
R:
AGACCAGGACCCTGTACTTGG
Band lengths:
106-119
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]