HsaINT0038499 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61938842-61939442:+
Coord C1 exon
chr20:61938842-61939000
Coord A exon
chr20:61939001-61939322
Coord C2 exon
chr20:61939323-61939442
Length
322 bp
Sequences
Splice sites
5' ss Seq
TAGGTGGGT
5' ss Score
5.56
3' ss Seq
GCCATGCCCCTGCTCCCCAGGCC
3' ss Score
7.98
Exon sequences
Seq C1 exon
CCGGCCCCCAGTTCCGCTGCCTGCCCCCCGTGCCTGCTGACATGGTCTTCCTGGTGGACGGGTCCTGGAGCATTGGCCACAGTCACTTCCAGCAGGTCAAGGACTTCCTGGCCAGTGTCATCGCACCCTTTGAAATCGGGCCGGATAAGGTCCAAGTAG
Seq A exon
GTGGGTGCTGGCCCGGCCCGCCTCCTGCCCCACCCGGGTGTGGTCCCCACAGCTCTGCCAGAGGAGGCTGTGACCTGTGGGGGTCCCCGTACCAGCCAGGGCTCTCACCTTGTGGGGTGGGACGCCTGCTCCACATGGGGTGTTCTGGGGACCCCTCCGTGTGGAGGCCCTGGCTCTGCAAGCGTCCTCTCCCTGGGGACTGGCTACTGTGGCCAGGTGACCCCACAGAGGCACGTGCAGCTCTCAGGTGTGGCCTTGTGCCAAGCTCCCTGGGCATCTCAGCATTGGAAACTCAGCCCGTGGCCATGCCCCTGCTCCCCAG
Seq C2 exon
GCCTGACTCAGTACAGCGGGGATGCTCAGACTGAGTGGGACCTGAACTCCCTCAGCACCAAGGAACAGGTGCTGGCAGCTGTGCGCCGCCTCCGCTACAAGGGGGGGAACACGTTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.096 A=NA C2=0.077
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(23.7=74.1)
A:
NA
C2:
PF0009223=VWA=FE(23.7=100)
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:
CCCCGTGCCTGCTGACAT
R:
CTGTGAACGTGTTCCCCC
Band lengths:
254-576
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)