HsaINT0038472 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63311625-63312055:+
Coord C1 exon
chr20:63311625-63311748
Coord A exon
chr20:63311749-63311915
Coord C2 exon
chr20:63311916-63312055
Length
167 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
GGCTCTGCTGTGCTTTGCAGCCA
3' ss Score
8.14
Exon sequences
Seq C1 exon
GTGCAGGTCGGGCGGCCCGAGGTGCTGCTGGATGGCCTGGAACCTGGCAGGGACTATGAGGTCTCGGTGCAGAGCCTGCGAGGCCCTGAGGGCAGCGAGGCCCGGGGCATCCGTGCCAGGACCC
Seq A exon
GTGAGTGCTCCAACCCCGGCTGCCTGCCCACAGGCGGGTGCCCCATCTTGTTCCTCAGCCTTCCATGGCATGGGAGACCTCAGGCCCCCTCGGTCCCAGCCACTGCCCACCCTTGCCCCTGCCATGGAGGCCGCGTGCTGGCCTTGAGGCTCTGCTGTGCTTTGCAG
Seq C2 exon
CCACCCTGGCCCCCCCGAGACACCTGGGCTTCTCAGACGTGAGCCACGACGCGGCACGAGTGTTCTGGGAGGGTGCCCCGAGGCCTGTGCGCCTGGTCAGGGTCACCTATGTGTCCAGCGAGGGTGGACACTCGGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.857 A=NA C2=0.532
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(41.2=78.6)
A:
NA
C2:
PF0004116=fn3=PU(53.1=91.5)
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:
GAGGTGCTGCTGGATGGC
R:
CCCCGAGTGTCCACCCTC
Band lengths:
243-410
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