HsaINT0039821 @ hg19
Intron Retention
Gene
ENSG00000092758 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:2219]
Coordinates
chr20:61460807-61461033:+
Coord C1 exon
chr20:61460807-61460851
Coord A exon
chr20:61460852-61460979
Coord C2 exon
chr20:61460980-61461033
Length
128 bp
Sequences
Splice sites
5' ss Seq
CGGGTATGT
5' ss Score
8.79
3' ss Seq
CAGCTCTCCTTCCTCTACAGGGC
3' ss Score
9.45
Exon sequences
Seq C1 exon
GGCCTCCCTGGACGAGCGGGGTCCAAAGGCGAGAAGGGAGAACGG
Seq A exon
GTATGTGGCTGCAGCCGCTTTCTCTCTGGGAGGGGAGGCGAGGGGCCGGGAGGCAAGGGGCTGGGGGGCCAGCGACCTGGCCCCAGTGCAGGTGTAGGCAGGCACTCACAGCTCTCCTTCCTCTACAG
Seq C2 exon
GGCAGAGCTGGGGAGCTGGGTGAGGCCGGCCCCTCTGGAGAGCCAGGCGTCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092758-COL9A3:NM_001853:20
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(15.6=100),PF0139113=Collagen=PU(6.0=33.3)
A:
NA
C2:
PF0139113=Collagen=FE(18.9=100),PF0139113=Collagen=FE(20.5=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)