RnoINT0039318 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176507411-176507896:+
Coord C1 exon
chr3:176507411-176507540
Coord A exon
chr3:176507541-176507753
Coord C2 exon
chr3:176507754-176507896
Length
213 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
TTATACACCTTGTCTTCCAGAGA
3' ss Score
7.85
Exon sequences
Seq C1 exon
ATTCAGGTTCCTGGGAACGTTACCTCAGCTACTCTGGGCCCACTTTCTTCCTCTACCGTGTACACCATCCGAGTCACCTGTTTTTACCTCAGGGGTGGTTCCTCCGTGCTGACTGGCCATGTGACCACAC
Seq A exon
GTGAGTCTATGAAGTCAAGGCTGGGGTACAGCCGGACTGTGTCCTTATGTCCTGCTAAAGGGCCTATGTTGGGTGTCTGTTCTGGCTGTACTAGGTCAGGTGGGGACAAGTGTCTGACAAGGGTCAGGGACATTCCTGCATGTAGCTGACCCTTGTCTAAAAGCAACAGCTAAGGTCAATATCTATACTCCATTTATACACCTTGTCTTCCAG
Seq C2 exon
AGAAAGCGCCTAGCCCTAGCCAGTTGTCGGTGACGGAGCTCCCGGGAGATACAGTAAAGCTGTCATGGTTGGCCACTGCCTTGTCTGGTGTACTTGTTTATCAGATCAAGTGGATGCCCTTGGGAGAGGGGAAGGCCCATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.295 A=NA C2=0.229
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.6=77.3)
A:
NA
C2:
PF0004116=fn3=PU(53.7=91.7)
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:
GTTCCTGGGAACGTTACCTCA
R:
GCCTTCCCCTCTCCCAAGG
Band lengths:
260-473
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]