RnoINT0040494 @ rn6
Intron Retention
Gene
ENSRNOG00000009531 | Col9a3
Description
collagen type IX alpha 3 chain [Source:RGD Symbol;Acc:1310255]
Coordinates
chr3:176110506-176111078:+
Coord C1 exon
chr3:176110506-176110559
Coord A exon
chr3:176110560-176111024
Coord C2 exon
chr3:176111025-176111078
Length
465 bp
Sequences
Splice sites
5' ss Seq
GCGGTATGT
5' ss Score
9.45
3' ss Seq
CCCCCCCTGTTATTTTTTAGGGT
3' ss Score
12.57
Exon sequences
Seq C1 exon
GGTCCCATTGGGTTTCGGGGCCCCCCAGGGATCCCAGGAGCACCTGGGAAAGCG
Seq A exon
GTATGTATCATCTGTCTAGGCTGGAAGGTGGACTTCGCACCAGCCCAGACCCTCTGACCCCTCCACTTTACCATCTGTTGCTGGTTCACATACATGCCACCCTTTGTCCCACTGGGCTGCCCCTACTCTGTCCCAGGATGAGCTGCCCATAGATACATGGGGGACTTGGAACGTAGCAAGGGGTGGTATATCCATGAGGTCCAGGGCACACAAGAAGTAGCACAGGACAATGTGGCATGCTGGTGACAGACAGCTGGAGCATGGGCATGGGGCATCTGGCCTGGTGGCACGTCACTGTCCCATGTGACCTTCTACAGCAGGGGACTGCCTGTGACCAGGTCTAGAGAGCTAAGCCAGGCACAACCTGGAGGGGCTTCAGTCAAGACCTGGAGGGGCTTCAGTCAAGACCCTGACTTCTCTGTGTTGTTAACCCTGTCCCTATCCCCCCCCCCTGTTATTTTTTAG
Seq C2 exon
GGTGACAGGGGTGATAGGGGACCAGAAGGGTTCCGTGGCCCTAAGGGTGACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009531:ENSRNOT00000013105:15
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(21.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.5=100),PF0139113=Collagen=PU(18.5=94.4)
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]