HsaINT0038488 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61956793-61957073:+
Coord C1 exon
chr20:61956793-61956846
Coord A exon
chr20:61956847-61957019
Coord C2 exon
chr20:61957020-61957073
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-COL20A1:NM_020882:28
Average complexity
IR-S
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(29.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(22.4=100),PF0139113=Collagen=PU(11.8=44.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)