HsaINT0038475 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63312792-63313249:+
Coord C1 exon
chr20:63312792-63312934
Coord A exon
chr20:63312935-63313116
Coord C2 exon
chr20:63313117-63313249
Length
182 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
TGGGGCTCTCCTCTCCCTAGATC
3' ss Score
10.6
Exon sequences
Seq C1 exon
AGAAAGCTCCCAGCCCAAGCCAGCTGTCCATGACGGAGCTGCCAGGGGATGCAGTCCAGCTGGCGTGGGTGGCCGCAGCCCCGTCTGGCGTGCTTGTCTACCAGATCACGTGGACGCCCCTGGGAGAGGGGAAGGCTCACGAG
Seq A exon
GTGGGCAGGGGTGGGTTTGTCCTTCCGAGGGGCCCCCCGTGGGCCCCTAGTCCTGAAGCCAAAGTCTAGGGCTCAGAGCCATATGTGCGCCCACCCTGTCTCCCAGGGATGCCTCACTGCCCGGCCCCCCAACCTGAGGACCCCACTGCACCCGGTGACCCCTGGGGCTCTCCTCTCCCTAG
Seq C2 exon
ATCTCTGTCCCAGGGAACCTCGGCACGGCCGTCCTGCCTGGCCTAGGGAGGCACACAGAGTACGACGTCACCATCTTGGCCTACTACAGGGACGGGGCCCGCAGTGACCCTGTGTCCCTCCGCTATACCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.271 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.7=91.7)
A:
NA
C2:
PF0004116=fn3=PD(43.9=80.0)
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:
CCAAGCCAGCTGTCCATGAC
R:
GTATAGCGGAGGGACACAGGG
Band lengths:
257-439
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