HsaINT0038502 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61940685-61941267:+
Coord C1 exon
chr20:61940685-61940849
Coord A exon
chr20:61940850-61941109
Coord C2 exon
chr20:61941110-61941267
Length
260 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CACTCCCGCTACTCCAGCAGCAG
3' ss Score
1.65
Exon sequences
Seq C1 exon
GTGTGAAGAACGCCGATGAGGCTGAGCTGAGGCTCCTGGCGTCCCCGCCGAGGGACATCACCGTCCACAGCGTGCTGGACTTCCTGCAGCTCGGCGCGCTGGCTGGCCTGCTCAGCCGTCTCATCTGCCAGAGGCTCCAGGGTGGGAGCCCGCGGCAGGGCCCAG
Seq A exon
GTGAGGGGCAGGGTCACCCGCACAGGCTGCAGCCCCCCCGGCTGCTTTGGGCAAAGGGTTGGGGGGACGCTGTGGCTCCCGTGTGGTACCTGAGGCCGGCTCCTGTGGCTCTGAGGGGGTCTGCAGCACCCCCTTACATCTGTCCACAGAAGGGCTGGGGAGCAGCTTTCCTGTCCCTCCTGTGAGTGGCCACCAGGGGGAGCGTGGACACAGCTGCCCGTGCAGTGACCACCTGCCCCCCACTCCCGCTACTCCAGCAG
Seq C2 exon
CAGCGGCTCCAGCCCTGGACACCCTCCCTGCCCCCACCAGCCTGGTCCTGAGCCAGGTGACCTCCTCCAGCATCCGCCTGTCCTGGACTCCAGCCCCCCGGCACCCCCTCAAGTATCTGATCGTTTGGCGAGCCTCTAGAGGTGGCACCCCCAGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.132
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(19.5=58.9)
A:
NA
C2:
PF0004116=fn3=PU(53.8=81.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTGAAGAACGCCGATGAGG
R:
CTCTAGAGGCTCGCCAAACG
Band lengths:
306-566
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)