HsaINT0038479 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61926450-61929372:+
Coord C1 exon
chr20:61926450-61926541
Coord A exon
chr20:61926542-61929261
Coord C2 exon
chr20:61929262-61929372
Length
2720 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
ACTATGTCCTGTTTCTGTAGCAA
3' ss Score
7.42
Exon sequences
Seq C1 exon
CCCGAGCACCATGAGCTCCGGAGACCCTGCACACCTCGGCCTCTGCCTCTGGCTGTGGCTGGGCGCCACCCTGGGAAGAGAGCAAGTTCAAG
Seq A exon
GTAAGGACACTGGCAGTGGGCCCCTGCTTGCCCCGAGGCCACGCCTGCCCCACCAGTGCCCACGCGGGACGAGCCCTCCGCCCCTGAGCCCCGTCTTCCTCCTAAGTTGAATGCGTGCTGAATTCACAGCAGCTCCCACAACAAAGGCAAGACGGGAGGGAGCGTGTGCTCCCGCCAAACCTTCAGCCTCGCCTTGGGAGCACATCTCTGTGGTTTAGTTCTCTGTTATATTAATGCTTGGCCGAGAGTTATTCCACGAACACCTTTCGGAGCAGTCTCTAGGAAGCAGGAGGCTGGGGTAAAGATGGAGCCGCCTTCCCTTCCCTCCTGCCTGCTTCCCACCGCCGCCTCCCACTGGTGTTTTGGGCACATAGCCCTCTGGCTTCTCTCGGTGCGGCACTCGCATTTCCACGCAGCACCACCCCCTCCGTGCGCATCCCTGGGCGACAGCACCACGTCCTCAGAAGGCCCCTCCAGTCTGGCTGCTACTGGTTGGGGCGTTTGGGTAACGTAGGGCACCGCCCATGGCAGCAAAGGGAAATGGCAGAGGATGCTGTGGGCTCACCTGTCTGAGCAGCTTCTTCCTCCTGTTGAGAAATGTGGGTTTAGATTGACTCTAGGAAGGTGAATTTCCGTGTCTATGGAGAAGGCTCCGGGGCCTCGGCCACGCTGTAAACTTGTCCCTGGGCTGGGCCAACGCGGCGCCTCCCGGCACCTGCAAGCTCCTGGGAGGTTCCGGGCTCCCACTGAGCGATGGTTTTGTTCCGCTGGGGTGAAAGGCAGCTCCCCCTTCTACTGTGCGTTTAAAGCACCCCCACCAGGGCCTGACAGGCCGGGGCGAGGGAGCCTCCAGGTGCCGCTGCCATTGCAGAAGGGCGGGTGAGATGCGGGAGCCCCGGTGTAGCGTGGAGCCGCCTGTTGAGACCCTTCCGGGTTTCACGGCTTGTCTTGCCATGCTGATGTGCCAGGTTTGCCCTGCACACAGGCAACAGACCATTGCATGAGCAGGTGCCTTGGTCCCCTCAGCTCAGACAGGGTAACCCTGCCCTGGGGCCAGTGGGGGCTGAGATTTCAGTTTGAAAGAAGCTTGCACTGTCAATTTGAGCCAAATCAGTAAGTTGCTTCTACAGAAACAACTTGAGTTTAGGCGAAGGCAAATCTAGTTCTATCTAGTTCAGGATTCAGCATGATGGGGCCACCCCTCACAAGGGCCTTTCGGGGGCCATTGAGTCCCTGAGGACAGCCAGGTGGGCTGGGGGCACTGAGTCCAGCCCAGGACGGGTGGGAGCCCACACGCTGGGGCAGCCCTTCCCAGGATGGCCCAGGCTGGGTGCGGCCACAGTCCAGGGAGGGGAGCGTGGTCCTGGGTGGGGCCCTTCCCACCAGCCGCTGTCTGCCCAGTGCCCTGCTCAGGCCCCAACAGTGCTGTCCTCCAGCAGGGAGCTGGGGAAGGGGTCCCTGACGTTCTCAGGCAGAGTGGAGCAACAGAAGGCTCTTCACAAGCAGGGGCTGCGGGAGGGGCCCTGCTCACAGCTGGCCTTCAGAGCCCCCTCCTCATCCCCCACACATTCCTGCCTTTCAGCCCCATCCGGAGACCCGGCCCAGCTGCTGCCTGCTCTGAATGGGTCATTGTGTCTGCCCCAGTGCCCCCCAGCCCCTGCTCTTCCCCCCGAGCCCCAGCTTTCCGGGGGGCAGCCCAAAGAAGCCCATCTCTGTCCCCATTTTCCAAAAATAGCTGCCCCTACTGCAGAGCCCCGGAAGCTTTCAGGGGGCACCAACCCTCTCCAGAGCCCTGGGAGGTTGGCCAGGCCCCTGCCGCCCCCTCTTCCTCTCAGATGGCCTGGACACCCATCCCCCATCGCGGGAGGCAGCCTCGTCTTGGCATGGACGCACACATGTACCAACGTGCACACACGTGCCAATGTGCACACACTTCCAGTGTGGGATTCTGCACCCACACTCCCCACTGAGGCGGCACGTGCACCTGGCAGTGACCTTGGCAGCTAGGGGTCTGCAGCTGCATGGCCACTTGTCCTGGGGACCCAGCCCAGGGGACTCAGCCCAGGGGCCCCAGCCCAGGGGACTTAGCTCAGGGGACCCAGCCTGGGGACTCAGCCCAGGGGCCCCAGCTCAGGGGACTTAGCTCAGGGGACCCAGCCCAGGGGACCCAGCTCAGGGGACTCAGCTCAGGGGACCCAGCCCAGGGGACTCAGCCCAGGGGCCCCAGCCCAGGGGACTTAGCTCAGGGGACCCAGCCCGGGGACTCAGCCCAGGGGCCCCAGCTCAGGGGACTCAGCTCAGGGCCCTGGGCAGGTTGCCAGCTGCTGTGTTGGCTCGGGGCCTCCGATCATCAGTGGGGTGGTTGCTGTCCTCCCAGACATGGGCCTGAGCCTCTTCCTGGTGGGAGGACCCCCGGAGAGCCAGGCTGGGGCCTCCCTGGGTGGGACTGGACTCCCTCTCACCAAAGCTACCAGGGTGGCCCTGTGACTGCGGACCCCGGGGAGGGCCGGGTTCTCCTCAGCGCCCAGGCGAGGCCTCGTATCCCCAAGTGGGGCTGAGTCCGCCTCAGACACCCTGGGTGGGCTTCTGTCTCTTCGGGGTCCCCCGGGATAGGACTGTGTTCCTCCCAAATGCTGAGGGCAGGATGCCTGTACCCCCACAGCTGATTAGGTGGATGGGGAGGCCAGGTCAGTCCTGACCACTATGTCCTGTTTCTGTAG
Seq C2 exon
CAAGCGGTCTCCTGAGGCTGGCTGTGCTGCCTGAGGACCGGCTGCAGATGAAGTGGAGAGAGTCGGAGGGGAGCGGCCTCGGCTACCTGGTGCAGGTGAAGCCCATGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.105
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004116=fn3=PU(46.7=92.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)