HsaINT0039818 @ hg38
Intron Retention
Gene
ENSG00000092758 | COL9A3
Description
collagen type IX alpha 3 chain [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr20:62828764-62828976:+
Coord C1 exon
chr20:62828764-62828817
Coord A exon
chr20:62828818-62828922
Coord C2 exon
chr20:62828923-62828976
Length
105 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGC
5' ss Score
6.1
3' ss Seq
CCCAATCTCTGTCCTCACAGGGA
3' ss Score
9.45
Exon sequences
Seq C1 exon
GGCATGCCGGGCAAGGACGGCCAGAATGGCGTGCCAGGACTCGATGGCCAGAAG
Seq A exon
GTTGGCATGGGGCTCAGGGTGTGACGGGAGGGAGGGGGCTGGAGGGGAGTTCGGCCTCCCGAGGCCTCAGCCTCCCCTTCCGCACCCCAATCTCTGTCCTCACAG
Seq C2 exon
GGAGAGGCTGGTCGCAACGGTGCTCCGGGAGAGAAGGGCCCCAACGGGCTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092758:ENST00000343916:18
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(18.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.9=100)
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:
GCAAGGACGGCCAGAATGG
R:
CCGTTGGGGCCCTTCTCT
Band lengths:
91-196
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