RnoINT0039337 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176523176-176523912:+
Coord C1 exon
chr3:176523176-176523247
Coord A exon
chr3:176523248-176523876
Coord C2 exon
chr3:176523877-176523912
Length
629 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
CCTTTAACCTCCTGCTACAGGGT
3' ss Score
7.52
Exon sequences
Seq C1 exon
GGATTCCAGGGCTTGGCAGGGGCCAGCGGTACCAGTGGAGAGCAAGGGCCCCCAGGAGCTGTGGGTCCCACA
Seq A exon
GTAAGTACCCCCTCACACACACCTCCAGCAAGGCAGCCAAGCAACAGGGAATGTACAGGCTCAGGATCAGGGCTTCCCTGATTGAAGAGCTGCCTGTTCAGAGCTTCCTGTGGCTTCCATGGGGCACAGAATTGGAAGGAGGCTGCAGCTGACTTATGGGAATCCAGCTCCCTGGAAGGTCACCGTTACCTTCAGTAAAGAGGAATAGGGTGTCAGCAGTTCAGACCCCTGGAGTGGACTCCGTAGCATGGGCACAGCGGAGGGAGAAGCAGGATGATGTGACTTTCTTGGCTCAGCCTGTCTCTGGGCCAAGGGAGGGTCTGTTCTCTAGACAGTGTTTCAGCTGGTTGGGAGCTCTGCCCATGCTTCCCAGTACAAAATGCCAGCCGGGGATAGGGTCTTTGCAGGTGGAGCATTCCCAGCTCCACATGGGACTTTCCCTGCTGTGGATGTCCAGCTTCACTTGTTCATTCTGGGCTGGCGCTGAGGGCAAACACTTCTGGAGCTTGGCAGTTGGGTTGGGGCTTTGGCACCACAACCCCTGTGGAGTCGAGCCTGACATAGGTTGCCATGCCTGCGACTCCTTGCCTCTATCCTGACAGCTCTTTCCCTTTAACCTCCTGCTACAG
Seq C2 exon
GGTCTACCAGGGTCCAAAGGTGAACGAGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:32
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(39.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]