HsaINT0038491 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63326096-63326823:+
Coord C1 exon
chr20:63326096-63326149
Coord A exon
chr20:63326150-63326751
Coord C2 exon
chr20:63326752-63326823
Length
602 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGGC
5' ss Score
7.26
3' ss Seq
TGACTTCTGTGTCTATGCAGGGG
3' ss Score
10.3
Exon sequences
Seq C1 exon
GGAATGAGAGGCCTGGAGGGAACTGCTGGCCTGCCTGGACCCCCTGGCCCCAGG
Seq A exon
GTAGGCACCGACCTCCCATGACCCCGACCCCCACCCAGGGTTCCTGTGTTCCAGGGGTCAGGCAGAGGCCAGTCTGAACACCAGCTGCCACCCCTAGGTTACCCCAGGAAGTGCCTGGGAGGGCCTCACTTCTGCTGGAACTTTCTGCAGGGCCCTGTGGGTGGGTGAGCGTCTGCCCAGGAGCACTGCATGCTCCCAAGTGAGGGCTCTGTGCTGAGGACTCAGTTCCTGGGAGACCTTGGAGGGGGGTCTCCTGGCATCGGCCTCGGGCTGAGTGCTGGGCAGGCCAGGTTGCCTCCCTGCAAGCGCCACTTTAGGGGAAGCCCAACTTGCAGTCACACTGGAGCAGCTGGCACAGCTGGGGACGTTTAGAGCAGCGTGCTGACAGTGCTGGAGGAGGGGTGCAGGGCATGGGGAGCCAGGGCCTGGAGGCAGGGGAGGCACCACCTGCCGGAGGAATGGCCTGAAGGAGGCTGGGGCCAGCCAGGCATCCACCGCCCTTGTCAGGTCAGGGGGCCCCTGGGACATCTGGGAACCAGGGCTGAAGTGGGAGCAGATTTGCTGGGGGCCCAAGCCAAACCCTGACTTCTGTGTCTATGCAG
Seq C2 exon
GGGTTCCAGGGCATGGCAGGGGCCAGGGGCACTAGTGGAGAGCGAGGACCTCCAGGGACCGTGGGGCCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:29
Average complexity
IR
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:
PF0139113=Collagen=PD(23.7=77.8),PF0139113=Collagen=PU(28.8=94.4)
A:
NA
C2:
PF0139113=Collagen=FE(33.8=100)
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