RnoINT0040488 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176102351-176103034:+
Coord C1 exon
chr3:176102351-176102416
Coord A exon
chr3:176102417-176102965
Coord C2 exon
chr3:176102966-176103034
Length
549 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATAATTTATCTCCATTTCAGAAA
3' ss Score
8.74
Exon sequences
Seq C1 exon
ATGACCGGAGCGCCTGCCCTAGCCCTGCTGCTGCTGGGGCAGCTCCTGACGGCCACCTCCGCGCAG
Seq A exon
GTGAGCGCGGGCCCGCGGGTGCTTATGGGGTCGGGGATAGGGCCGGACGTCGAACCGTGCAGCCTGGGACAGACAACTCAAGCCCCTTGGGCCAACCCTTGAGTCCGGCCGCTAAGGACCCTCGAGGACATCTGTGGCAGCCTCTTCGTCGCCTCGCTCCAGTTGACGAGTTCTGGTGATGCAGCTGAGCCCCACGGACACCAGGACATGTCAGCCATGATCCTGGGCTTCCACTTGTCTTCACCCAACCGGGTCAGGCCGCTGCCAAGCGCTGCCACCACTGCCACCACGCTCAGAACACACAATGTTGCCTTTGTTCCTGGAGACTCCCTGCGGGGCCCGCAGCACAGCCACTCCTGGCTCGAACGAGGATAAACTGCCTAGGCGCCAGGCTCCAGCGCAGGAAACTTTGGGGTTTTTTAAGGCAGGCAGGGAGGAGGGTCATGAGCCACTGTCACAGGCCCCAGAGTTTCTTGGGCTAGGGAAGTTGGGACAGGAGGGCTGACATGTTGGGAAAGAGGCCTATCTAATAATTTATCTCCATTTCAG
Seq C2 exon
AAAGTGGGACCTCGAGGCCCCCCTGGTCCCCAAGGGCCTCCTGGAAAACCCGGCAAGGATGGCATCGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(1.7=4.5)
A:
NA
C2:
PF0139113=Collagen=FE(37.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
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]