RnoALTD0007321-3/3 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176521752-176522274:+
Coord C1 exon
chr3:176521752-176521805
Coord A exon
chr3:176521806-176522069
Coord C2 exon
chr3:176522221-176522274
Length
264 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGGT
5' ss Score
8.1
3' ss Seq
TTCCCTCCTCTGCTCATCAGGGA
3' ss Score
7.86
Exon sequences
Seq C1 exon
GGCCTCTCTGGCCAGCAAGGCATCCCTGGGAAAACTGGCCTACAAGGACCAAAG
Seq A exon
GTATTGGCTCCAGGCCCAGTGGGTGATGAGTGGGAGAGAGAGGGCCCAGGTAGAGTCTTGGAGACAGAAGCTACAAGGATTGAGGAAGTAGAGAGGCTTCCTTCTCCACCCGAGGCTTCATCTATCTTACTCCCTAAAGCCTGGCTTAGGACAAAAGCTCTCTCAGCCCACACTGAGGGTAAATGCTGTCACCCCGAGGTGGGGTGAAGGGAGGCAGCTACTCTAATCAGAGCTGGGGAAAGCTCCACATCTCACCTTACCAGG
Seq C2 exon
GGAATGAGAGGACTGGAGGGACCTGCTGGGCTGCCTGGACCACCTGGCCCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326-35-46,36-46,37-46-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(30.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(20.0=61.1),PF0139113=Collagen=PU(28.8=94.4)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]