RnoINT0040509 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176119438-176120284:+
Coord C1 exon
chr3:176119438-176119492
Coord A exon
chr3:176119493-176120101
Coord C2 exon
chr3:176120102-176120284
Length
609 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
GGCACTCTGTTTTCCAAAAGAGC
3' ss Score
3.28
Exon sequences
Seq C1 exon
GGCAAGGAAGCCAGTGAACAACGCATCAGGGAGCTGTGTGGGGGGATGATCAGTG
Seq A exon
GTGAGTGTCCTGTGCATACTCTACCCCTCACACAGCTCTGCCCTTTCTGTTCTCCCTACCTTACCTGTCCTCTGGCCTCAAGGAGGACTACCCTCCTCCCAGTGTCTGACACAATGAGGGTACTCAGAGGAGCCCCAACTAACTACTGAGGGCAACAATTACAAGAAAGAAACCGGGTGGTGGTGGTGCATGCCTTTAATCCCAGCACTTGAAAGGCAGAGGCAGGCAGATCCCTGAATTGGGAGCCTGCCTGGTCCACAGAGTTCCAGGACATCCAGGGCTACACAGAGAAACCCTGTCTCAAAAAACAAACAAACAAACAAACAAACAAACAAACAATTACAAGGAAGAAACCACTGTGCCCTTTGGCTGGGAGGGACACTTCCCCTGAGTGGCTTTGAACTTCTCAATCCAGCATGAGAGGTAGTCTAAGAGAAGGGGCCCTCCCGTCTCCCCTGGGATAATCTAGAACAGATAAAACAATTGTCTTTGGTCAGTAAGTGAAAATCCCCTTCTGACAGAGGGCTGGCTGTATTATACTTTGCATGAAGATGTTTTGGTAATCCTCTCTGAAGTATGTTATGTGCTTGGCACTCTGTTTTCCAAAAG
Seq C2 exon
AGCAAATTGCACAGCTGGCTGCACACCTGAGGAAGCCCTTAGCACCAGGCTCCATTGGCAGGCCTGGTCCAGCTGGCCCCCCAGGCCCTCCAGGCCCCCCAGGCTCCATTGGCCACCCTGGCGCTCGGGGTCCTCCTGGATACCGTGGTCCCACTGGGGAACTAGGAGATCCTGGACCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:29
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(9.4=31.6)
A:
NA
C2:
PF0139113=Collagen=PU(75.8=75.8)
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:
AAGGAAGCCAGTGAACAACGC
R:
GGTCCAGGATCTCCTAGTTCCC
Band lengths:
230-839
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]