HsaINT0038494 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61959431-61959850:+
Coord C1 exon
chr20:61959431-61959479
Coord A exon
chr20:61959480-61959682
Coord C2 exon
chr20:61959683-61959850
Length
203 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
GACACCCCTCCTCCCCACAGCAC
3' ss Score
9.96
Exon sequences
Seq C1 exon
GGCGAGCCGCAGTCCCTTGCCACCCTCTACCAGCTTGTGAGCCAGGCCT
Seq A exon
GTGAGTCTGCCATTCAGAGTGAGTGAGGCCAGCAGCCCTGCACCTGTGCCTACCACACCTGTCTGTCCTCACACTGGCCAGGCCGAGGGAGGCCGCCTTCACCCATCGTTAGCACACCTGGGCCAGGTGTCCTGGCGTGGCCTGCACAGGCCTCGCATCCCCGGGTCCCCACTGTGTCCTGCTGACACCCCTCCTCCCCACAG
Seq C2 exon
CACACGTGTCAAAGTTCGACTCCTTCCACGAGAACACCAGGCCCCCCATGCCCATCTTGGAGCAGAAGCTGGAGCCGGGCACTGAGCCCCTGGGGTCCCCTGGCACCCGCAGCAAGGCCCTGGTTCCTGGAGAATGGGGGCGTGGTGGCCGCCACCTTGAGGGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:33
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.841 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(6.8=23.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTCCCTTGCCACCCTCTAC
R:
CTCTGCCCTCAAGGTGGC
Band lengths:
207-410
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)