RnoINT0039327 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176514932-176515465:+
Coord C1 exon
chr3:176514932-176515041
Coord A exon
chr3:176515042-176515306
Coord C2 exon
chr3:176515307-176515465
Length
265 bp
Sequences
Splice sites
5' ss Seq
AAGGTCCTG
5' ss Score
-0.19
3' ss Seq
ACTTACTATGGTTTCTGCAGGTA
3' ss Score
8.71
Exon sequences
Seq C1 exon
CTGGCAGAAAGTCTCTGACTTACTTCAACCATGATTCCAGAGCAGCCTTGCAGGAGATCACCTTTGACCTGCAGGATGCAAAGAAGATTTTCTTTGGAAGCTTCCACAAG
Seq A exon
GTCCTGGGAACTGCCTGAGCCCCGACCCTCTGGCCTATACCTCCCTGCATGTGGTTGTCTCCTCTACCCTGTTCTGATTGTCCATCCTTAATTTGGGTCAGAGAGCAAACTCTTCTTTTTGGGAGGCTCCTGCAGCAGCTTTCTCTGGGAAGCTAAGGCCCCAATAGGTTCCACAGTGGGGTCAGACTCACAGGAGTCTTTGCATTGGTCCTCTTAATCTGTTTTGATGTGATCTGGGATGGGAGACTTACTATGGTTTCTGCAG
Seq C2 exon
GTACATATAGCTGTAGGCCACTCTAAGATCAGACTTTACGTGGACTGTCGGAAGGTGGCTGAGCGGCCCATTGGGGATGCTGGCAGCCCACCCACAGCTGGTTTCATCACACTAGGGAGGCTAGCCAAGGCCAGAGGGCCACGGAGCAGCTCAGCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.283
Domain overlap (PFAM):
C1:
NO
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:
AGTCTCTGACTTACTTCAACCATGA
R:
TGTGGCTGAGCTGCTCCG
Band lengths:
260-525
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]