HsaINT0038493 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63327952-63328145:+
Coord C1 exon
chr20:63327952-63327987
Coord A exon
chr20:63327988-63328078
Coord C2 exon
chr20:63328079-63328145
Length
91 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TGCACCACCTTCCCTTCCAGGGC
3' ss Score
10.41
Exon sequences
Seq C1 exon
GGACTGCCAGGGCCCAAAGGGGAACGAGGAGAGAAG
Seq A exon
GTAAGTGAGGCTGAGATCTTTGGCTCACTTGGGATCTCCTGGGAAGGCACCTGCCACACGGGTCCCAAAGCTGCACCACCTTCCCTTCCAG
Seq C2 exon
GGCGAGCCGCAGTCCCTTGCCACCCTCTACCAGCTTGTGAGCCAGGCCTGTGAGTCTGCCATTCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:31
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=0.834
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(16.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(5.9=23.5)
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:
GACTGCCAGGGCCCAAAG
R:
GAATGGCAGACTCACAGGCC
Band lengths:
99-190
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