HsaINT0038484 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63320039-63320368:+
Coord C1 exon
chr20:63320039-63320197
Coord A exon
chr20:63320198-63320290
Coord C2 exon
chr20:63320291-63320368
Length
93 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
CCGGCTCCCCTGCGTTGCAGTTT
3' ss Score
7.47
Exon sequences
Seq C1 exon
GTGCACGTGGCTGTGGGCCGCTCCAAGGTCAGGCTCTATGTGGACTGCCGGAAGGTGGCTGAGCGGCCCCTTGGGGAGATGGGCAGCCCACCCGCTGCGGGCTTCGTCACGCTGGGGAGGCTGGCCAAGGCCAGGGGCCCCCGGAGCAGTTCGGCCGCG
Seq A exon
GTGAGTTGGGCCCTGCCCACCTGCTGGGCCACGCTGGTGGGGGCTGGCAGCCTCTCTGAGCCCCGGGGCTGAGCCGGCTCCCCTGCGTTGCAG
Seq C2 exon
TTTCAGCTCCAGATGCTGCAGATCGTGTGCAGTGACACCTGGGCCGATGAGGACCGGTGCTGTGAGCTCCCTGCCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.154 A=NA C2=0.077
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GTCAGGCTCTATGTGGACTGC
R:
GGTGTCACTGCACACGATCTG
Band lengths:
171-264
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