HsaINT1008128 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63309333-63309915:+
Coord C1 exon
chr20:63309333-63309497
Coord A exon
chr20:63309498-63309757
Coord C2 exon
chr20:63309758-63309915
Length
260 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CACTCCCGCTACTCCAGCAGCAG
3' ss Score
1.65
Exon sequences
Seq C1 exon
GTGTGAAGAACGCCGATGAGGCTGAGCTGAGGCTCCTGGCGTCCCCGCCGAGGGACATCACCGTCCACAGCGTGCTGGACTTCCTGCAGCTCGGCGCGCTGGCTGGCCTGCTCAGCCGTCTCATCTGCCAGAGGCTCCAGGGTGGGAGCCCGCGGCAGGGCCCAG
Seq A exon
GTGAGGGGCAGGGTCACCCGCACAGGCTGCAGCCCCCCCGGCTGCTTTGGGCAAAGGGTTGGGGGGACGCTGTGGCTCCCGTGTGGTACCTGAGGCCGGCTCCTGTGGCTCTGAGGGGGTCTGCAGCACCCCCTTACATCTGTCCACAGAAGGGCTGGGGAGCAGCTTTCCTGTCCCTCCTGTGAGTGGCCACCAGGGGGAGCGTGGACACAGCTGCCCGTGCAGTGACCACCTGCCCCCCACTCCCGCTACTCCAGCAG
Seq C2 exon
CAGCGGCTCCAGCCCTGGACACCCTCCCTGCCCCCACCAGCCTGGTCCTGAGCCAGGTGACCTCCTCCAGCATCCGCCTGTCCTGGACTCCAGCCCCCCGGCACCCCCTCAAGTATCTGATCGTTTGGCGAGCCTCTAGAGGTGGCACCCCCAGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.132
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(19.5=58.9)
A:
NA
C2:
PF0004116=fn3=PU(53.8=81.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTGAAGAACGCCGATGAGG
R:
CTCTAGAGGCTCGCCAAACG
Band lengths:
306-566
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains