HsaINT1008127 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63328079-63328498:+
Coord C1 exon
chr20:63328079-63328145
Coord A exon
chr20:63328146-63328330
Coord C2 exon
chr20:63328331-63328498
Length
185 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
GACACCCCTCCTCCCCACAGCAC
3' ss Score
9.96
Exon sequences
Seq C1 exon
GGCGAGCCGCAGTCCCTTGCCACCCTCTACCAGCTTGTGAGCCAGGCCTGTGAGTCTGCCATTCAGA
Seq A exon
GTGAGTGAGGCCAGCAGCCCTGCACCTGTGCCTACCACACCTGTCTGTCCTCACACTGGCCAGGCCGAGGGAGGCCGCCTTCACCCATCGTTAGCACACCTGGGCCAGGTGTCCTGGCGTGGCCTGCACAGGCCTCGCATCCCCGGGTCCCCACTGTGTCCTGCTGACACCCCTCCTCCCCACAG
Seq C2 exon
CACACGTGTCAAAGTTCGACTCCTTCCACGAGAACACCAGGCCCCCCATGCCCATCTTGGAGCAGAAGCTGGAGCCGGGCACTGAGCCCCTGGGGTCCCCTGGCACCCGCAGCAAGGCCCTGGTTCCTGGAGAATGGGGGCGTGGTGGCCGCCACCTTGAGGGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.834 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(5.9=23.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTCCCTTGCCACCCTCTA
R:
CTCTGCCCTCAAGGTGGC
Band lengths:
226-411
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains