HsaINT0039839 @ hg38
Intron Retention
Gene
ENSG00000092758 | COL9A3
Description
collagen type IX alpha 3 chain [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr20:62822111-62822632:+
Coord C1 exon
chr20:62822111-62822164
Coord A exon
chr20:62822165-62822590
Coord C2 exon
chr20:62822591-62822632
Length
426 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
GCTGTCTCTTTTTGTCTTAGGGA
3' ss Score
10.23
Exon sequences
Seq C1 exon
GGACCTTCTGGACTCCCCGGCCTCCCTGGTCCCCCAGGACCTCCCGGACCCCCT
Seq A exon
GTAAGTACTGGGCAGAGGCTCTAAGAAGTGCTGGGCATGGACTAGGACACTGGGTTGGACCCTCCCCATTCCCCCTCCCCAGGCTCCATGCCCCTCCGAGATCTCCTAACCCTAACTTGGCCACTCCCAGGAACAGTCAATGGTGGGGGCAGTGGCTGTGGCTAGGCCAGCCAACTTGGGGATGGTCAGGACTCAGGTCCCCATGGCCATCCTGCCCCAAGGACAGGTGGATTCTGTCGTTGTCACATGCCCTGTGGGTGGGCCAGCAGCTCCCAGCACTGGCCACTTGGGGGACAGGATGAAGGGTCTCCAAGTCCCCTGGTGGATGGGGAAGGTTGTGGTCCGTCAGAGAGTGGGTGGGTGGGTTGGGTGGCTGCAGGTGGCTGGGGAGGGCGGGAGAATGTCAGCTGTCTCTTTTTGTCTTAG
Seq C2 exon
GGACACCCAGGAGTCCTCCCTGAAGGCGCTACTGACCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092758:ENST00000343916:9
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(29.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(17.5=71.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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