HsaINT0038471 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61942746-61943100:+
Coord C1 exon
chr20:61942746-61942891
Coord A exon
chr20:61942892-61942976
Coord C2 exon
chr20:61942977-61943100
Length
85 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
GGGACGTCATGTCTCTGCAGGTG
3' ss Score
7.66
Exon sequences
Seq C1 exon
CACCTCTGCCTCCGCCCCGGGCGCTGACCCTGGCCGCAGTGACGCCCAGAACCGTCCACCTCACCTGGCAGCCCTCGGCCGGGGCCACCCACTACCTGGTGCGATGTTCTCCTGCTTCCCCCAAGGGTGAAGAGGAGGAGCGAGAG
Seq A exon
GTGAGCTGGGCCGGGGGGTGGCGGGGGAGGCAGAGGAGTGGGGCAGAGCGAGTGGGGGCTGGCCTGGGACGTCATGTCTCTGCAG
Seq C2 exon
GTGCAGGTCGGGCGGCCCGAGGTGCTGCTGGATGGCCTGGAACCTGGCAGGGACTATGAGGTCTCGGTGCAGAGCCTGCGAGGCCCTGAGGGCAGCGAGGCCCGGGGCATCCGTGCCAGGACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.469 A=NA C2=0.857
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(56.2=91.8)
A:
NA
C2:
PF0004116=fn3=PD(41.2=78.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAACCGTCCACCTCACCTG
R:
TGCACCGAGACCTCATAGTCC
Band lengths:
170-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)