HsaINT0038484 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61951391-61951720:+
Coord C1 exon
chr20:61951391-61951549
Coord A exon
chr20:61951550-61951642
Coord C2 exon
chr20:61951643-61951720
Length
93 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
CCGGCTCCCCTGCGTTGCAGTTT
3' ss Score
7.47
Exon sequences
Seq C1 exon
GTGCACGTGGCTGTGGGCCGCTCCAAGGTCAGGCTCTATGTGGACTGCCGGAAGGTGGCTGAGCGGCCCCTTGGGGAGATGGGCAGCCCACCCGCTGCGGGCTTCGTCACGCTGGGGAGGCTGGCCAAGGCCAGGGGCCCCCGGAGCAGTTCGGCCGCG
Seq A exon
GTGAGTTGGGCCCTGCCCACCTGCTGGGCCACGCTGGTGGGGGCTGGCAGCCTCTCTGAGCCCCGGGGCTGAGCCGGCTCCCCTGCGTTGCAG
Seq C2 exon
TTTCAGCTCCAGATGCTGCAGATCGTGTGCAGTGACACCTGGGCCGATGAGGACCGGTGCTGTGAGCTCCCTGCCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:24
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.151 A=NA C2=0.077
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=FE(43.0=100)
A:
NA
C2:
PF0221019=Laminin_G_2=PD(6.6=30.8)
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:
GTCAGGCTCTATGTGGACTGC
R:
GGTGTCACTGCACACGATCTG
Band lengths:
171-264
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)