RnoINT0039339 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176523993-176524301:+
Coord C1 exon
chr3:176523993-176524059
Coord A exon
chr3:176524060-176524133
Coord C2 exon
chr3:176524134-176524301
Length
74 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGT
5' ss Score
6.05
3' ss Seq
ACTGATGTCTCCTTCCCCAGCAC
3' ss Score
7.62
Exon sequences
Seq C1 exon
GGAGAGCCACAGTCCCTTGCCACCATCTTCCAGCTGGTGAGCCAGGCCTGCGAGTCAGCCATACGGA
Seq A exon
GTGAGTGAAAACCTCCCCTCCGGACCCCACCCCTATTGGTGAGGCTGGGCCCCAACTGATGTCTCCTTCCCCAG
Seq C2 exon
CACACGTGATGAAGCTGAATTCCTTCCTTCATGAGAATGCCCGTCCCCCGATGCCCTTCATGGCAGAGACAGCCAAGCTAAGCAGACCCAGAGCTATAGATCCTGGATTACACAACAAGGCTCTACTTCCTGGAGACTGGGGACATATCCTCCACCATGAGGATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.435 A=NA C2=0.877
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(6.8=17.4)
A:
NA
C2:
NO
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:
GCCTGCGAGTCAGCCATAC
R:
ATGTCCCCAGTCTCCAGGAAG
Band lengths:
168-242
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]