RnoINT0040507 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176118976-176119253:+
Coord C1 exon
chr3:176118976-176119008
Coord A exon
chr3:176119009-176119106
Coord C2 exon
chr3:176119107-176119253
Length
98 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TTCCTCTTGTTTTTCTGCAGTCC
3' ss Score
10.2
Exon sequences
Seq C1 exon
GGTCCTAATGGCCCCGTTGGACAAAAAGGAGAG
Seq A exon
GTGAGTACATCCCAGATACTGATATGTGGTGGCCACTCATTCCTGAGGTCCAGGCCTGGAGGACTCACTCTGACCTGCTTCCTCTTGTTTTTCTGCAG
Seq C2 exon
TCCGGCAGCCGAGGGGAACTGGGCCCCAAAGGCATCCAGGGCCCCAATGGTACCAGTGGGGTCCAGGGTGTGCCTGGTCCCCCAGGTCCACTGGGCTTCCAAGGCGTGCAGGGTGTCCCAGGCATCACGGGGAAACCTGGAGTTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:27
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(13.2=100),PF0139113=Collagen=PU(10.9=63.6)
A:
NA
C2:
PF0139113=Collagen=PD(13.2=20.4),PF0139113=Collagen=FE(75.0=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:
GCCCCGTTGGACAAAAAGGAG
R:
AACTCCAGGTTTCCCCGTGAT
Band lengths:
167-265
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]