HsaINT0038501 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63308542-63309497:+
Coord C1 exon
chr20:63308542-63308706
Coord A exon
chr20:63308707-63309332
Coord C2 exon
chr20:63309333-63309497
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:ENST00000422202:7
Average complexity
IR
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