HsaINT0038501 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61939894-61940849:+
Coord C1 exon
chr20:61939894-61940058
Coord A exon
chr20:61940059-61940684
Coord C2 exon
chr20:61940685-61940849
Length
626 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
ACCTCCCTCCTCACGAGCAGGTG
3' ss Score
6.73
Exon sequences
Seq C1 exon
GCCTTGCCCTGACCCACGTGCTGGGGCAGAACCTGCAGCCGGCGGCTGGCCTCCGTCCAGAGGCAGCCAAGGTGGTGATTCTGGTGACGGACGGCAAGTCCCAGGACGATGTGCACACTGCTGCCCGTGTCCTCAAGGACCTGGGCGTGAACGTCTTCGCTGTGG
Seq A exon
GTGAGCACCATGCGGCTCCCCCGGCCCTGGAGTCTCACCGCCGGGTGGGTTTAGGGTCGCAGCAGGGAGCTTGCATTGGGCACCTGGTCCCTGAGCCCCAGCTTCCACATCTGCGGCACGGAGCTGCACGCAGAGCCAGGCACCGCCTGGCACTCAGAGGCGATGGCACAGGCGGGCTGCTCCTTTCCAATCGCCTGGTGTTTGGTGCCCTCCGTGGAACCACCCCAACCCTCCCCCTGTGGCGTGAACTTCCCTGGTGAGATATTCACTGAGCAGCTCCAGCTGCCCCCTCTGGCCACCATCCCTGTGCCTGGTGACTCCCGCCTGCTGTGCCCTGGCAAGGAGCTTCCTGGCATCCTCCAGGGCCTGGGACTCACAGGCGAATCAACTCTGTCCTGTGGGGAGGAAACCCCAGATTTCGAGGCAGGAGTCCCAGGAGCACAGACCCTTCCTTGATGCCCCCAACCCCTCGGGAGCGCCTGGCCCAGCATGTGGGTGGCAGGTGGGCCGAGTACAGCCCATAGGCCTCTTTACTCCTGACCCAGTCTCCATGGAGACCCCCACCGCAGGTGGCCCCGTCGGGTGACCCCAGTGCAGGCCAACCCCACCTCCCTCCTCACGAGCAG
Seq C2 exon
GTGTGAAGAACGCCGATGAGGCTGAGCTGAGGCTCCTGGCGTCCCCGCCGAGGGACATCACCGTCCACAGCGTGCTGGACTTCCTGCAGCTCGGCGCGCTGGCTGGCCTGCTCAGCCGTCTCATCTGCCAGAGGCTCCAGGGTGGGAGCCCGCGGCAGGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.071
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(32.5=100)
A:
NA
C2:
PF0009223=VWA=PD(19.5=58.9)
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:
CTTGCCCTGACCCACGTG
R:
CTCCCACCCTGGAGCCTC
Band lengths:
311-937
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)