RnoALTA0009770-2/4 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176508890-176510054:+
Coord C1 exon
chr3:176508890-176509019
Coord A exon
chr3:176510016-176510018
Coord C2 exon
chr3:176510019-176510054
Length
3 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGT
5' ss Score
8.02
3' ss Seq
GACCTTCCATATCCTCTCAGCAG
3' ss Score
5.37
Exon sequences
Seq C1 exon
ATCTCTGTACCAGGCACCAGGAGCCATGTTGTACTTCGTGATCTGATGTCTGCCGCCAAGTACAGGGTCCTGGTCTCAGCTGTCTATGGAGCAGGGGAGAGCATGGCAGTGTCTGCCACATACCGCACAG
Seq A exon
CAG
Seq C2 exon
CCTGCCCAGCCCTGCACCCGGACAGTTCCCTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326-23-30,23-29,23-28,23-27-2/4
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.2=79.5)
A:
NA
C2:
NO
Main Skipping 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:
GGTCCTGGTCTCAGCTGTCTA
R:
GAGAGGGAACTGTCCGGGTG
Band lengths:
99-102
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]