RnoINT0040497 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176112603-176112811:+
Coord C1 exon
chr3:176112603-176112656
Coord A exon
chr3:176112657-176112757
Coord C2 exon
chr3:176112758-176112811
Length
101 bp
Sequences
Splice sites
5' ss Seq
AAGGTCGGT
5' ss Score
7.13
3' ss Seq
CGTATTCACTATCCTTGCAGGGA
3' ss Score
8.03
Exon sequences
Seq C1 exon
GGCATGCCAGGCAAGGATGGCAAGGACGGTGTGCCGGGACTTGACGGTGAGAAG
Seq A exon
GTCGGTACCTGGCTGGATGCTTGCCGGGAGGAGGTGGAGGAGTTCAGCTTCCCAAGGCCCCAGCATCATTTATCCTTATACCGTATTCACTATCCTTGCAG
Seq C2 exon
GGAGAGGCTGGTCGCACTGGTGCCCCAGGAGAAAAAGGCCCCAATGGGCTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:18
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(18.5=100),PF0139113=Collagen=PU(4.9=27.8)
A:
NA
C2:
PF0139113=Collagen=FE(18.5=100),PF0139113=Collagen=FE(16.7=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:
GCATGCCAGGCAAGGATGG
R:
ATTGGGGCCTTTTTCTCCTGG
Band lengths:
98-199
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]