HsaINT0038495 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61959683-61961013:+
Coord C1 exon
chr20:61959683-61959850
Coord A exon
chr20:61959851-61960936
Coord C2 exon
chr20:61960937-61961013
Length
1086 bp
Sequences
Splice sites
5' ss Seq
GAGGTACTG
5' ss Score
7.67
3' ss Seq
TGCCCTCCCTTTCCTCGCAGGGG
3' ss Score
12.48
Exon sequences
Seq C1 exon
CACACGTGTCAAAGTTCGACTCCTTCCACGAGAACACCAGGCCCCCCATGCCCATCTTGGAGCAGAAGCTGGAGCCGGGCACTGAGCCCCTGGGGTCCCCTGGCACCCGCAGCAAGGCCCTGGTTCCTGGAGAATGGGGGCGTGGTGGCCGCCACCTTGAGGGCAGAG
Seq A exon
GTACTGGGCTCCTGGCTCTTGGGGAGGGAGTTGTGGCCGGTGGGGGCGCCGGTTGTCCCCTGGTCCTGGGGCTGGGGCTTCAATCTGTGTCAGCACAGCAGCTCCTGCTGGAGATGCCACTGTCCAGCCTCTGGGGTGCTGGGGTGAGGACACGGGGCTTCCCTGAGCCCACACAAAGCCAGTCATGGCAAAGAGGTCAGCCTCGGCCTGGCCTTCCAGGGCCCTCAAGATGACCTCTTCCCCAGTCTTCAGGAAACATGAGCTGCCTGCTTAGGGCCACACAGGAGAGCCCAGCCTACCTCCCATCCTTCCTCCCGCCCTCCCGCCCTCCTGTCCTCCTTGTCCTCCCCACTCCCGCCCTCTTATCCTCCTGGCTGCTGCTTCCTCCGCCTCTCCCCACCCAGCGCACAGTCGCAGGCTCCCGTGACCTTGTTGGTGCTCCTCCTCCTCTGAGGCAGCAGCGGTGGGTCATGACTTGGACGCTGAGATGGAGGAGAGGCTGATTCGGGGAGCTGGAGCTGGAGAGGGGCGTCCACGGGGAGAACAGACGGGGGATGACCCAGCCAGACGAGGACTGAGTTCTGCACTGGCCGGGGCAGCAGCGGGGGCATCTCTGCTCTGTTCGGGCATCGGCTGAATCCCACCCCTCATCCCACAGACGTCTCAGGAAACTGGGGGCAACCTGGGGGGAGCCCCGTGGGCTGTGGGAACCCCTGCCCCCGGCTTGGAAGCTGCCCACAGTGGCCTGGTTGCAGCCTGGCAGATGAGGGGTACATCACTACTCAGAATAAACGGCCCCCTCTGCACCCACCTGTCTAGATGAGGGTGACAGGCACTATCACAGGGCCCCCACCTGACGCCTTCCCACCTGGCCATGCCCCCCCAGAACTGTCATGGAGCCCAGGAGGCGCCTGTGTGGAGCACGGGGACCTGGCACGCTGCTGCCCCTAGATCTCAGACTCCCATCTAAGGACCAGACCTGCTGCCTGTGCCCAGGGAGGGGCCCTGACACCCTCTGTCCCCGTCAGAACAGGGCCCCAAGCCACTGCATTGCTCCGTCCTCACATGCCCTCCCTTTCCTCGCAG
Seq C2 exon
GGGAGCCTGGAGCTGTTGGTCAGATGGGCAGCCCTGGGCAGCAGGGGGCTAGCACCCAGGGCCTCTGGGAGTGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:34
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACACGTGTCAAAGTTCGACTCC
R:
GTCACTCCCAGAGGCCCTG
Band lengths:
242-1328
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)