HsaINT0038497 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63305417-63306060:+
Coord C1 exon
chr20:63305417-63305560
Coord A exon
chr20:63305561-63305880
Coord C2 exon
chr20:63305881-63306060
Length
320 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
CTCTTTGTGTCTCCCTGCAGTTG
3' ss Score
12.43
Exon sequences
Seq C1 exon
GGGACTCGGAACAGGAGGTGATACTGACCACCAAGACCCCTAAGGCCACAGTGGGGGGCCTGAGCCCCTCCAAGGGCTACACCTTGCAGATCTTCGAGCTCACTGGCTCTGGGCGCTTCCTGCTAGCTCGGAGGGAGTTTGTGA
Seq A exon
GTAAGTCCACCGTCTGCCAGCTGGGTACCCACTCCTCCAGGCCGGGTCCCACCCTCCTCTGGGCTGGGGTCCCACCCTCCTCCAGGCTGCGTTCCAGCCCCAGGGGTGGGTATGTGTGAAGCAGTTCTGGGCTGTGCTAGGGGCAGGTTCAAGTCCCGACTCACCAGCAAGGCTGCCTTGCCCCTGACATCTTTGCATGCCTCCCAGGCTCCTGGGCCCTCAGCACCCACAGATGCGCCCTTGAAGGGGTGTATGTGCAGCTGCCCCAGTGGACCAGGCCCTCCACTCCCACCCTGATGGCTCTTTGTGTCTCCCTGCAG
Seq C2 exon
TTGAGGATCTGAAGAGTAGCTCCCTGGACAGGAGCAGCCAGAGGCCCCTCGGCTCTGGAGCCCCGGAGCCCACCCCCTCCCACACGGGGAGCCCAGACCCTGAGCAGGCTTCTGAGCCCCAAGTTGCCTTCACACCAAGCCAGGATCCGCGCACTCCTGGTGGGTCAGAGTGGAGAGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.347 A=NA C2=0.842
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(52.0=79.6)
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:
GGACTCGGAACAGGAGGTGAT
R:
CTCTCTCCACTCTGACCCACC
Band lengths:
322-642
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