HsaINT0039815 @ hg19
Intron Retention
Gene
ENSG00000092758 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:2219]
Coordinates
chr20:61458119-61458646:+
Coord C1 exon
chr20:61458119-61458172
Coord A exon
chr20:61458173-61458592
Coord C2 exon
chr20:61458593-61458646
Length
420 bp
Sequences
Splice sites
5' ss Seq
GCGGTACGT
5' ss Score
10.27
3' ss Seq
CCCCACCTCATCCTTTCCAGGGT
3' ss Score
8.77
Exon sequences
Seq C1 exon
GGTCCCATTGGGTTCCGAGGGCCGCCTGGGATCCCAGGAGCGCCTGGGAAAGCG
Seq A exon
GTACGTGTGTCAGTGGACGGTGGGCGCCATGCCTCGTGACCTCTCTCCCCTTTCCCTCTGCTCCTCTCAGACGCCCCCAGCCCCACTGGGGCCCCTCTTCTGTGGCTGAGCTGTTCCCTGGACACCCTGGGAGGGCTTGTGGCATGGGTACGGGGGTGCTTACCAATGGAATCCATTCTTTGTGAGACATTCGCCTCCTTTCTGGTTCTGGACGTGGAATGAGGGGTCACCATCGTCCCTCTGGCACCTCCAGCCATCTCTGACCACTCCTGGAGGGCCCAGGCCTGGAGGGGCCCCCATCCCACTCTCTGACCACTCCTGGAGGGCTGTCCCCCGCCCGGGCCTGGAGGGGCCCCCGTCCTACTCTCCGACCAACTCCATGGTGTTAACTCTGTCCCTGCCCCACCTCATCCTTTCCAG
Seq C2 exon
GGTGACCGAGGCGAGAGGGGCCCAGAAGGGTTCCGCGGCCCCAAGGGTGACCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092758-COL9A3:NM_001853:15
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=FE(15.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(15.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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)