RnoINT0040518 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176107292-176107654:+
Coord C1 exon
chr3:176107292-176107345
Coord A exon
chr3:176107346-176107612
Coord C2 exon
chr3:176107613-176107654
Length
267 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TATCTCTCTGTCTGTTGAAGGGA
3' ss Score
8.53
Exon sequences
Seq C1 exon
GGACCCTCTGGACTTCCAGGCCTGCCTGGCCCCCCAGGACCTCCTGGACCTCCT
Seq A exon
GTAAGTACTGGAGGGGACCCTATCAGGCATCCTAGACTAACTGGGCTGGGCCCTACCCTAGTCCCTGCCCAGGTTCTGTGCCATTCCCCAGAAGCAGGTGGGATACAGGAACTGCTGTAGCAAGGTCACCTCGCCCCAAGGTCAGCAGTGCCTTGCACTGGCCACTGGGGAGAAAAGATTGAGGATTTCAAGTCCCCTGTTAGATTAAAGTCAAGGACAGGGTGTGGAAGGGTGGATACACACCAGCTATCTCTCTGTCTGTTGAAG
Seq C2 exon
GGAAACCCTGGAGTCCTCCCTGAAGGTGCTACTGATCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:9
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(29.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(17.2=71.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]