HsaINT0038474 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63312420-63312934:+
Coord C1 exon
chr20:63312420-63312549
Coord A exon
chr20:63312550-63312791
Coord C2 exon
chr20:63312792-63312934
Length
242 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
TGTGTCTCCACTTCCTTCAGAGA
3' ss Score
8.9
Exon sequences
Seq C1 exon
ACAGAGGCTCCTGGGAACGCCACCTCGGCCACGCTGGGGCCTCTCTCTTCCTCCACCACCTACACTGTCCGTGTCACCTGCCTCTACCCTGGGGGTGGCTCCTCTACGCTGACTGGCCGGGTGACCACCA
Seq A exon
GTGAGTGGGGAGAGGCTGGGGCTGGGGGTCCAGCAGGGTTTCTGTGTCCTTCTGCCCTGCTAGACAGTTCACATCAAGTGTTTTGGGAGCCTGCCCTGGGTCAGTGCTGAGCCAGGTGGGGATGGGCACCCGGACGGGTGTGATGGATGGGGGTATAGGGTGCTCCTGGGTGTGGCTGCCCCTCCTCTGAGGTGCCCAGGCTCAGGGGCTACACCCCCAGCCTGTGTCTCCACTTCCTTCAG
Seq C2 exon
AGAAAGCTCCCAGCCCAAGCCAGCTGTCCATGACGGAGCTGCCAGGGGATGCAGTCCAGCTGGCGTGGGTGGCCGCAGCCCCGTCTGGCGTGCTTGTCTACCAGATCACGTGGACGCCCCTGGGAGAGGGGAAGGCTCACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.545 A=NA C2=0.271
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(44.4=81.8)
A:
NA
C2:
PF0004116=fn3=PU(53.7=91.7)
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:
ACAGAGGCTCCTGGGAACG
R:
CTCGTGAGCCTTCCCCTCTC
Band lengths:
273-515
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