RnoINT0040508 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176119107-176119492:+
Coord C1 exon
chr3:176119107-176119253
Coord A exon
chr3:176119254-176119437
Coord C2 exon
chr3:176119438-176119492
Length
184 bp
Sequences
Splice sites
5' ss Seq
CCGGTTCGT
5' ss Score
5.83
3' ss Seq
TGAACCTGGGTGAATTTCAGGGC
3' ss Score
5.81
Exon sequences
Seq C1 exon
TCCGGCAGCCGAGGGGAACTGGGCCCCAAAGGCATCCAGGGCCCCAATGGTACCAGTGGGGTCCAGGGTGTGCCTGGTCCCCCAGGTCCACTGGGCTTCCAAGGCGTGCAGGGTGTCCCAGGCATCACGGGGAAACCTGGAGTTCCG
Seq A exon
GTTCGTTGCTTTTTCTTTCTCTCGTGTTGTGGGTTTTGGACTTGTGCTGGGTTTAGATCATGGTTTCATTTTGTTTTGTTTTTTGTTTCTTGTGAACTGTCGTTGGTTTGGGGAGTGAGGTGCTGGGTAAGTCAGGGTTACTGGTGCACTGCCCCACCTGCTGATGAACCTGGGTGAATTTCAG
Seq C2 exon
GGCAAGGAAGCCAGTGAACAACGCATCAGGGAGCTGTGTGGGGGGATGATCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:28
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(13.2=20.4),PF0139113=Collagen=FE(75.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(9.4=31.6)
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:
GCAGCCGAGGGGAACTGG
R:
CCCCACACAGCTCCCTGAT
Band lengths:
186-370
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]