RnoINT0039334 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176499931-176500470:+
Coord C1 exon
chr3:176499931-176500074
Coord A exon
chr3:176500075-176500314
Coord C2 exon
chr3:176500315-176500470
Length
240 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
AGTCTCTCCTCTGTCTGCAGTTG
3' ss Score
8.27
Exon sequences
Seq C1 exon
GGGACTTGGAGCAGGAGCTGGTACTGACCACCAAGACCCCCAAAGCCACTGTGGGTGGCCTGAGCCCTTCCAAGAGCTACACCTTACAGATCTTCGAGCTCACTGACTCTGGGCCTGTCCTGCTAGCACGAAGGGAGTTTGTAA
Seq A exon
GTAAGTCCTCCTGCAGCCAGATGGGTGGATTTGGTTGGAAGGCTTCTGGCTTGTGCCCTGAAGCATTTTGCCTGTGAAGTGCTTGGGTCTTTTTTCCTGTTCCCGGCATTGCTGCTCATCTCCCATGAGGCAGACAGCAAGTCTGTCGATTTGCCTTCCAGGAAGTGCACAAACCCCTAAGCTCTAAGCCCCTGCTCCTACACTGGGCTGGTGTCCTGACAGTCTCTCCTCTGTCTGCAG
Seq C2 exon
TTGAGGATCTAAAGAGCCAATCTTTGGGCAGAGGAAGCCGGAGGCTGGCAGGAGCCACCCTGGAGCCTCCCTCCTTCCCTCTGAGGGACCCAGACTCTGAGAAAACATCTGAGCCCAGCATTGCCTTCACCTCAAGCAGGGACCTTCCCATTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.102 A=NA C2=0.566
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(50.6=79.6)
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:
GGGACTTGGAGCAGGAGC
R:
GGAAGGTCCCTGCTTGAGGT
Band lengths:
292-532
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]