RnoINT0039332 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176521433-176521653:+
Coord C1 exon
chr3:176521433-176521528
Coord A exon
chr3:176521529-176521599
Coord C2 exon
chr3:176521600-176521653
Length
71 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGT
5' ss Score
8.6
3' ss Seq
CAGTCCATCTTCCCCTCCAGGGG
3' ss Score
8.61
Exon sequences
Seq C1 exon
GGAGAGCCTGGCCCACCTGGACAAACAGGACCCGAAGGCCCTGGAGGTCAGCAGGGGTCACCAGGGACCCAGGGCCGTGCAGTCCAGGGACCCATG
Seq A exon
GTAGGTACCGCTCTATACAGGTGTTCTCTCTTGTCCTTCTTCCCCACCTCTCAGTCCATCTTCCCCTCCAG
Seq C2 exon
GGGCCACCAGGAGCCAAAGGAGAGAAGGGGGATCACGGCCTCCCGGGCTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(47.5=87.5),PF0139113=Collagen=PU(10.9=18.8)
A:
NA
C2:
PF0139113=Collagen=FE(30.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAGCCTGGCCCACCTG
R:
GGCCGTGATCCCCCTTCT
Band lengths:
135-206
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]