HsaINT0038469 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61941110-61941862:+
Coord C1 exon
chr20:61941110-61941267
Coord A exon
chr20:61941268-61941732
Coord C2 exon
chr20:61941733-61941862
Length
465 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CCTTGCCCACTCTGTTCCAGGTG
3' ss Score
11.36
Exon sequences
Seq C1 exon
CAGCGGCTCCAGCCCTGGACACCCTCCCTGCCCCCACCAGCCTGGTCCTGAGCCAGGTGACCTCCTCCAGCATCCGCCTGTCCTGGACTCCAGCCCCCCGGCACCCCCTCAAGTATCTGATCGTTTGGCGAGCCTCTAGAGGTGGCACCCCCAGGGAG
Seq A exon
GTGAGGGGGCCGGTATACAGGGCTCCCCGAGCCGGTCCTCAGCCGTAGTGAGATCTGATAAGCCAAAGGGAGGGCAGGAATAAAGGCCCACAAATAACTGGGTCCAGGCTGAGAAGGGGGTGTCGAGGGGCTGACAGCCCAGGGACTCACTGGGGAGCTGCGTCTGGGAGGCAGCCTGGGATGAGTGCATTTTAGTGGCCGAGGAGGGCAGAGCAGGGGGCGTTCCGAGGGTGCTGGGGTTAGGGTCAGACTCAGAGCGCCTTCTCCCTTTGATTGATCGATCGATGGATAATTGTGGTGGGCCTGGCACTGCTCTGTCGTAGGTACAGGGAGCCCAGGCCTGTGGGAAGTGGGGCACCCTGCGGGCCCCAGCTGAGCTCACACTCCAGCTGACGGAGTTCCTGTCCTGCTCCCCATCCCCCGGCACCCCCCTTCCTGGCTCCGTCCTTGCCCACTCTGTTCCAG
Seq C2 exon
GTGGTGGTGGAGGGACCCGCCGCCTCCACGGAGCTGCACAACCTGGCCTCCCGCACAGAGTACCTGGTCTCCGTGTTCCCCATCTATGAGGGCGGGGTTGGCGAAGGCCTGCGGGGCCTGGTGACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.132 A=NA C2=0.341
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=81.1)
A:
NA
C2:
PF0004116=fn3=PD(43.8=79.5)
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:
CAGCCCTGGACACCCTCC
R:
CTGTGGTCACCAGGCCCC
Band lengths:
279-744
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)