RnoINT0040516 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176106636-176106942:+
Coord C1 exon
chr3:176106636-176106659
Coord A exon
chr3:176106660-176106888
Coord C2 exon
chr3:176106889-176106942
Length
229 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
CTCTCTTTTACCTCCTCCAGGGA
3' ss Score
10.1
Exon sequences
Seq C1 exon
GGCAAAGGCCTCCCTGGACCTCCT
Seq A exon
GTGAGTATTTACTACCCTCTGGCCCCTCCCAAGCGTGTACATTCCCAGAGAAGCTCTCACTGAAGCCCATTTTCTCTGGGATATCCTAGATCATGGGGAGTGGTCTTCTTAGGGCTCATCCTGACTACTTCACATAGAGTCCTGGCTTTTCAAAGGGCAGATGGCACTGGTGGGATTCCCTTGTTCAGGGTCACAGGTTGCCCATCTCCCTCTCTTTTACCTCCTCCAG
Seq C2 exon
GGAGAGGCAGGAGTGAGTGGCCTCCCAGGTGGGATTGGTCTACGTGGCCCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:7
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=PD(3.0=25.0),PF0139113=Collagen=FE(12.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(29.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
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]