HsaINT0039829 @ hg19
Intron Retention
Gene
ENSG00000092758 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:2219]
Coordinates
chr20:61467539-61467884:+
Coord C1 exon
chr20:61467539-61467685
Coord A exon
chr20:61467686-61467829
Coord C2 exon
chr20:61467830-61467884
Length
144 bp
Sequences
Splice sites
5' ss Seq
CCGGTACGT
5' ss Score
10.49
3' ss Seq
ATGTGTGGGGTGAATTCCAGGGG
3' ss Score
4.73
Exon sequences
Seq C1 exon
TCTGGCAGTCGAGGGGAGCTGGGCCCCAAAGGCACCCAGGGTCCCAACGGCACCAGCGGTGTTCAGGGTGTCCCCGGGCCCCCCGGTCCTCTGGGCCTGCAGGGCGTCCCGGGTGTTCCTGGCATCACGGGGAAGCCGGGAGTTCCG
Seq A exon
GTACGTCGCTTTTCCGGCTTTTCCAGCTTTCACAGGGTTGAGATCGTGTTTTTTCCGGAAGGAAGTTACTTTGCGGGGTGACGGTGGGAATGCCTCACCGAGGCTGCCGCCCCCATGCTGACGAATGTGTGGGGTGAATTCCAG
Seq C2 exon
GGGAAGGAGGCCAGCGAGCAGCGCATCAGGGAGCTGTGTGGGGGGATGATCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092758-COL9A3:NM_001853:28
Average complexity
IR-C
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(10.8=16.3),PF0139113=Collagen=FE(76.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(7.9=26.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGGCAGTCGAGGGGAG
R:
CACACAGCTCCCTGATGCG
Band lengths:
187-331
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)