RnoINT0038894 @ rn6
Intron Retention
Gene
ENSRNOG00000000463 | Col11a2
Description
collagen type XI alpha 2 chain [Source:RGD Symbol;Acc:2373]
Coordinates
chr20:3855982-3856408:+
Coord C1 exon
chr20:3855982-3856035
Coord A exon
chr20:3856036-3856140
Coord C2 exon
chr20:3856141-3856408
Length
105 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CCCTCTCTGTCCCCACCCAGGGT
3' ss Score
10.07
Exon sequences
Seq C1 exon
GGCCCCGCTGGACCCAAAGGAGAGAAAGGTGTTCAGGGCCCTCCAGGACACCCG
Seq A exon
GTGAGTGAGGAGCGGCAACCAACCGGGCTCTGGCTGTAAGCACTCCATTGGGGCTATCCTTTACTCTGACAGGGACCTCACTGTACCCTCTCTGTCCCCACCCAG
Seq C2 exon
GGTCCCCCGGGCGAGGTGATCCAGCCACTGCCCATCCAGATGCCCAAGAAGACCCGGCGCTCTGTGGACGGAAGCAAACTGATGCAGGATGAGGAGGCCACACCCACTGGCGGTGCCCCGGGCAGTCCTGCAGGACTGGAGGAGATCTTCGGTTCACTGGACTCTCTGCGGGAGGAGATCGAACAGATGAGGAGGCCGACAGGGACCCAGGACAGCCCTGCCCGCACCTGCCAGGACTTGAAGCTGTGCCACCCAGAGCTTCCCGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000463:ENSRNOT00000045533:60
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=0.933
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(13.1=8.9),PF0141013=COLFI=PU(41.5=30.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGACCCAAAGGAGAGAAAGGT
R:
GGCCTCCTCATCTGTTCGATC
Band lengths:
243-348
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]