HsaINT0038471 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63311394-63311748:+
Coord C1 exon
chr20:63311394-63311539
Coord A exon
chr20:63311540-63311624
Coord C2 exon
chr20:63311625-63311748
Length
85 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
GGGACGTCATGTCTCTGCAGGTG
3' ss Score
7.66
Exon sequences
Seq C1 exon
CACCTCTGCCTCCGCCCCGGGCGCTGACCCTGGCCGCAGTGACGCCCAGAACCGTCCACCTCACCTGGCAGCCCTCGGCCGGGGCCACCCACTACCTGGTGCGATGTTCTCCTGCTTCCCCCAAGGGTGAAGAGGAGGAGCGAGAG
Seq A exon
GTGAGCTGGGCCGGGGGGTGGCGGGGGAGGCAGAGGAGTGGGGCAGAGCGAGTGGGGGCTGGCCTGGGACGTCATGTCTCTGCAG
Seq C2 exon
GTGCAGGTCGGGCGGCCCGAGGTGCTGCTGGATGGCCTGGAACCTGGCAGGGACTATGAGGTCTCGGTGCAGAGCCTGCGAGGCCCTGAGGGCAGCGAGGCCCGGGGCATCCGTGCCAGGACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.469 A=NA C2=0.857
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(56.2=91.8)
A:
NA
C2:
PF0004116=fn3=PD(41.2=78.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAACCGTCCACCTCACCTG
R:
TGCACCGAGACCTCATAGTCC
Band lengths:
170-255
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