HsaINT0039809 @ hg38
Intron Retention
Gene
ENSG00000092758 | COL9A3
Description
collagen type IX alpha 3 chain [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr20:62817062-62817635:+
Coord C1 exon
chr20:62817062-62817142
Coord A exon
chr20:62817143-62817566
Coord C2 exon
chr20:62817567-62817635
Length
424 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATGAGTTTTCTCCGTTTCAGAGA
3' ss Score
8.65
Exon sequences
Seq C1 exon
GCCATGGCCGGGCCGCGCGCGTGCGCCCCGCTCCTGCTCCTGCTCCTGCTCGGGGAGCTTCTGGCGGCCGCCGGGGCGCAG
Seq A exon
GTGAGCGCGAGCTCCGGGCTCTGAGGCTGGACGTGGAGCCGCGACCGCCCCAGCCCCGAACCCGCCACTCCGGGGTGCCCGGCGCAGCCTCGACGCCCCCAGCCCGTGTCGCCGTCGGGGCGCGGAGTCGCCAGCGCCTCGGGATGAGCCCCGTCCGGCCGCGTCCTCGATGGGTCCTCGCTGGCCCGGGTCGGCCGGCGCCGCCGCCTCCTCTGGGAGCACAAGGGGGCCTTTGTTCCCGCCGCCGGAGGGAGGCGGGGGACACACTGCGCGGGGGCGCCGGGCTCCGCCCGAGGCTTTGGGTCTCACCGAGGAGAGCGGCGGTCGTCGCAGGCCCCGGAGCCGCTCGGGACCCGGGAGGAGGGGACGCCGGGTCAGGCCCACGGGGGCACCTGCGCTCCTTAATGAGTTTTCTCCGTTTCAG
Seq C2 exon
AGAGTGGGACTCCCCGGCCCCCCCGGCCCCCCAGGGCCGCCCGGGAAGCCCGGCCAGGACGGCATTGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092758:ENST00000343916:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.221 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(3.3=7.7)
A:
NA
C2:
PF0139113=Collagen=FE(34.9=100),PF0139113=Collagen=PU(3.2=8.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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