RnoINT0039340 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176524134-176524761:+
Coord C1 exon
chr3:176524134-176524301
Coord A exon
chr3:176524302-176524683
Coord C2 exon
chr3:176524684-176524761
Length
382 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCA
5' ss Score
7.22
3' ss Seq
TTGTCCCCCTTTCTTCTCAGGTG
3' ss Score
11.56
Exon sequences
Seq C1 exon
CACACGTGATGAAGCTGAATTCCTTCCTTCATGAGAATGCCCGTCCCCCGATGCCCTTCATGGCAGAGACAGCCAAGCTAAGCAGACCCAGAGCTATAGATCCTGGATTACACAACAAGGCTCTACTTCCTGGAGACTGGGGACATATCCTCCACCATGAGGATGAAG
Seq A exon
GTATCAGGCTTCCTGCTCTTGGAAGGGATTCTAGAGGTAGACAGTGGCTGGTTCCCTGCACACACATGGGTGTTCGTGTGTGCATGTGCGTGCGTGTGCGTGTGTGCATTTGTGTGTATGTGTTTCCTCCTCATCAGCCTCTTTTACCCCAAAGATGTCTTAATGGGCACCTCATTTAGACGTTGCAGAGTCTACTCTGGCTGCTGAACCCACACTAATGGGGCTCAGTTCCTGATGGTCCTGGTACCATAGGCGCTTAGCCTTCAGCCAAGGGTCGAGCCTCACACTCATCCCAAGAGAACCCAGCCTCCCTCTGACAGACAGATCAGAGAAGCTGAAGCTGCTACGTCCCCAGTCCTTGTTTGTCCCCCTTTCTTCTCAG
Seq C2 exon
GTGAGCCTGTGGCTATCAGCCACACAAGCAAACCTGTACTGCAGGAGGTGCAGACCCCAGAGCCCCTGGAGTGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:35
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.877 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACACGTGATGAAGCTGAATTCC
R:
CTGTTCACTCCAGGGGCTCT
Band lengths:
246-628
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]