RnoALTD0007323-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176499945-176500470:+
Coord C1 exon
chr3:176499945-176500070
Coord A exon
chr3:176500071-176500074
Coord C2 exon
chr3:176500315-176500470
Length
4 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
AGTCTCTCCTCTGTCTGCAGTTG
3' ss Score
8.27
Exon sequences
Seq C1 exon
GAGCTGGTACTGACCACCAAGACCCCCAAAGCCACTGTGGGTGGCCTGAGCCCTTCCAAGAGCTACACCTTACAGATCTTCGAGCTCACTGACTCTGGGCCTGTCCTGCTAGCACGAAGGGAGTTT
Seq A exon
GTAA
Seq C2 exon
TTGAGGATCTAAAGAGCCAATCTTTGGGCAGAGGAAGCCGGAGGCTGGCAGGAGCCACCCTGGAGCCTCCCTCCTTCCCTCTGAGGGACCCAGACTCTGAGAAAACATCTGAGCCCAGCATTGCCTTCACCTCAAGCAGGGACCTTCCCATTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326-4-6,5-6-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.102 A=NA C2=0.566
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(50.6=79.6)
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:
CTGCTAGCACGAAGGGAGTTT
R:
CTCAGAGGGAAGGAGGGAGG
Band lengths:
106-110
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]