RnoINT0040500 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176113346-176113540:+
Coord C1 exon
chr3:176113346-176113390
Coord A exon
chr3:176113391-176113486
Coord C2 exon
chr3:176113487-176113540
Length
96 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
TTGTCTCTTCACTTGTATAGGGT
3' ss Score
7.97
Exon sequences
Seq C1 exon
GGGCTCCCTGGACGAGCAGGGTCCAAAGGCGAGAAGGGAGAAGTG
Seq A exon
GTAAGTGGCCGCTTTGCCCCAGAGAGGAGGCACAGCATTCAGTGCTGTGTGGGGGACAGAGGGGACATAGTACTCATTGTCTCTTCACTTGTATAG
Seq C2 exon
GGTAGAACTGGGGAGCTGGGCGAGGCTGGCCCCTCTGGAGAACCAGGTATTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:20
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(15.2=100),PF0139113=Collagen=FE(13.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(4.3=22.2),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:
CTCCCTGGACGAGCAGGG
R:
TGGTTCTCCAGAGGGGCC
Band lengths:
87-183
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]