HsaINT0038488 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63325441-63325721:+
Coord C1 exon
chr20:63325441-63325494
Coord A exon
chr20:63325495-63325667
Coord C2 exon
chr20:63325668-63325721
Length
173 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTG
5' ss Score
6.13
3' ss Seq
GCCCCTCTGTTCTCTCCCAGGGC
3' ss Score
11.45
Exon sequences
Seq C1 exon
GGTCCACCAGGGGTCAAAGGAGAGAAGGGAGACCATGGGCTTCCAGGCTTGCAG
Seq A exon
GTAGTGTGGCTGGGGCCAGGGGGCCACAGGGGTTGGTGGGGGTGGGGGAAGGACAGGGATGGAGATGGGGAGTGCCTGGGGGGCACAGGGGTTGGGGGTGAGGCCTCACAGGCAGGGCCACCTCTGGATGTGACCCTGGCCCCTGCCTGGCCGGCCCCTCTGTTCTCTCCCAG
Seq C2 exon
GGCCACCCCGGCCACCAGGGCATCCCCGGGAGAGTTGGCCTCCAGGGACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:27
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(28.8=100),PF0139113=Collagen=PU(21.6=61.1)
A:
NA
C2:
PF0139113=Collagen=PD(18.6=61.1),PF0139113=Collagen=PU(18.0=61.1)
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:
TCCACCAGGGGTCAAAGGAG
R:
CTTTGGTCCCTGGAGGCCAA
Band lengths:
106-279
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