RnoINT0038869 @ rn6
Intron Retention
Gene
ENSRNOG00000000463 | Col11a2
Description
collagen type XI alpha 2 chain [Source:RGD Symbol;Acc:2373]
Coordinates
chr20:3849836-3850058:+
Coord C1 exon
chr20:3849836-3849889
Coord A exon
chr20:3849890-3850004
Coord C2 exon
chr20:3850005-3850058
Length
115 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
CTGTCTGGCTGTCCCCTCAGGGA
3' ss Score
10.71
Exon sequences
Seq C1 exon
GGCCCCGCAGGGAAAGACGGGCTGCCGGGACACCCAGGCCAGAGAGGAGAAGTG
Seq A exon
GTGAGTGATTCCAGGGGTGTGGGGTGAGGAGGGGCTTGGGTCCTGCTGAGCCAGCTGCCCTGGTGCTGGGCTTCCTCTTGTCACCCACCCCTGTCCTGTCTGGCTGTCCCCTCAG
Seq C2 exon
GGATTCCAAGGGAAGACCGGCCCCCCAGGCCCGCCCGGAGTGGTGGGACCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000463:ENSRNOT00000045533:35
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=PU(2.9=11.1)
A:
NA
C2:
PF0139113=Collagen=FE(24.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGGAAAGACGGGCTGC
R:
CTGAGGTCCCACCACTCCG
Band lengths:
101-216
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]