RnoINT0039347 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176503605-176504144:+
Coord C1 exon
chr3:176503605-176503757
Coord A exon
chr3:176503758-176503974
Coord C2 exon
chr3:176503975-176504144
Length
217 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
CTGATTACCTTTCCTCACAGTCA
3' ss Score
7.93
Exon sequences
Seq C1 exon
GTGTGAAGAATGTCGACGAGGCCGAGCTGAAGCTCCTGGCATCCCAGCCGCTGGACATCACTGTCCACAACGTGCTGGACTTCCCTCAGCTGACCACCTTAGCCCCTCTGCTCAGCCGTCTTATTTGCCAAAAAATTCAGGGCAGAGGCCCAG
Seq A exon
GTAGGGATACAGCACCACAGTGACGGTGGAACAGGAAGATTGAGGCTATACTGGGGCAGTTTCATGGCCCAGAAGGGAGTGTAGCCTAAACCAGAGGGATTCCTCCTTGGATATGTTAAGGGTTGGGGTAGGGGGAGTTTCCTGTCCCTCCTGTATATGGCCACCAGGGGGAGTATGCGGACGTGCTTGCTTGGTTCCTGATTACCTTTCCTCACAG
Seq C2 exon
TCAAACCAGCGGCGGGTACTCGGATCCTGGACCCTCTCCCCACGCCCACCAGACTGACCCTGACCCACGTCACCTCATCCAGTATCCACCTGTCTTGGACTCCGGCCTTATACCCACCCCTCAAGTATCTAATTGTATGGCAGCCTTCTAGGGGTGGTGCCCCCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:9
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=0.123
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=71.2)
A:
NA
C2:
PF0004116=fn3=PU(53.8=75.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGAAGAATGTCGACGAGGCC
R:
CCCCTAGAAGGCTGCCATACA
Band lengths:
305-522
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]