RnoINT0039338 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176523877-176524059:+
Coord C1 exon
chr3:176523877-176523912
Coord A exon
chr3:176523913-176523992
Coord C2 exon
chr3:176523993-176524059
Length
80 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
AAATCATGTCCTCCTTCTAGGGA
3' ss Score
9.15
Exon sequences
Seq C1 exon
GGTCTACCAGGGTCCAAAGGTGAACGAGGAGAGAAG
Seq A exon
GTGGGTGAGTCCCATAATCTGGGGATCGGGACTCCCTTGTGGCAACTGCCACGAGTCCCCAAATCATGTCCTCCTTCTAG
Seq C2 exon
GGAGAGCCACAGTCCCTTGCCACCATCTTCCAGCTGGTGAGCCAGGCCTGCGAGTCAGCCATACGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:33
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=0.435
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(18.6=100)
A:
NA
C2:
PF0139113=Collagen=PD(6.8=17.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCTACCAGGGTCCAAAGGT
R:
TCCGTATGGCTGACTCGCA
Band lengths:
103-183
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]