HsaINT0039837 @ hg19
Intron Retention
Gene
ENSG00000092758 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:2219]
Coordinates
chr20:61452859-61453162:+
Coord C1 exon
chr20:61452859-61452882
Coord A exon
chr20:61452883-61453108
Coord C2 exon
chr20:61453109-61453162
Length
226 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
CTCTCTTTACTTCCCTCCAGGGA
3' ss Score
11.05
Exon sequences
Seq C1 exon
GGCAAAGGCCTCCCTGGACCCCCC
Seq A exon
GTGAGTACTGACAACCCTTGGGGCCCTGAGCAAGCACGCAAGTCCCGAGAGCCTGCCAGGCTGGGATGTCCCAAACCGTGCCTGGGGGTGGGGCTTCTCAGGGGCAGCCATCTGACCACCCCATACTTGGAGCCCCTCTCCCTTCGGAGGCGGCACACCAACCCTGGGTGGGGATCCTCGGGGCTTCCGGGTGCAGACCTCCCCACCTCTCTTTACTTCCCTCCAG
Seq C2 exon
GGAGAGGCAGGAGTGAGCGGCCCCCCAGGTGGGATCGGCCTCCGCGGCCCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092758-COL9A3:NM_001853:7
Average complexity
IR-S
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(3.5=25.0),PF0139113=Collagen=FE(12.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(29.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
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]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)