HsaINT0038470 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63310381-63311539:+
Coord C1 exon
chr20:63310381-63310510
Coord A exon
chr20:63310511-63311393
Coord C2 exon
chr20:63311394-63311539
Length
883 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
GTCCCTGCATGGCCCCCCAGCAC
3' ss Score
5.1
Exon sequences
Seq C1 exon
GTGGTGGTGGAGGGACCCGCCGCCTCCACGGAGCTGCACAACCTGGCCTCCCGCACAGAGTACCTGGTCTCCGTGTTCCCCATCTATGAGGGCGGGGTTGGCGAAGGCCTGCGGGGCCTGGTGACCACAG
Seq A exon
GTAGGTGGGGCAGAGGCAGCGGCCAGGTTCTGGGTGGGAGGCCCCACTCACGGCTGTCCCTTGGAGCCTGACACCCCAGGGCAGCATAGCGAGCAGCTCTGGATCTTAACCACCCACAGTTGGCACCATCCCCAGCTTGCTGTGTGACCAAGGCCGAGTCACTGGGCCCCTCTGACCCTGGGTGTTCTCTTCTGAACACCAGCTATACCGTTGGTGTCATCACCTCAACTGTAATCACAGCCCATTATGCTGCTTGTCCACAGTGTTCATGGAGCTCCCCCCTGCTTGGCCTCCAGCACGTGGCTTAGCTCGCTGGGTTCTTGGACCCCCAGGGACTGCCATGAGCCCGTCTGTAATAGCCTTGTTGAGATGTAATTTACACACCATACAACCTGCCCATTTAAAGTGTACAACTCCAGTGGCTTTGGTATATTCAGAGCTGTCACCCATGGCCACAGTTCATGTTAGATCATTTTCATCCCCCCAGAGGAACCCTGCACCCCTAAGCACCCGCCCCCCCAGCCACCCCAAGCCACCTTCTGTCTCTGGATGTGCCTGTCCCAGACGTTTCCTGCAGGTGGAATCACACAGTGCAGACTTTTGTGTCTGGGTGTTTCCCAAAGCCCTTTTCACCCCCCGGAGGCCACATTCCTCCCATGACCTCAAGGCAGATGGCCTTAGACAAAACTGTGGGGTGGCCTTGTGTCCCCAGAGCTGGAGCCACAAACCTTGGCCCAAGGTGAAGCCTGGGAAGTGCCACTTTGAATCCTGTGCACCTGCCAGGCGGTGGCCGTGCCCACCCACTCTGGTGTGAGGGTGCCCCGTGCGTGGGTGTGATCTCTGTGTGGGCTCCTTCCTAAAGTGTCCCTGCATGGCCCCCCAG
Seq C2 exon
CACCTCTGCCTCCGCCCCGGGCGCTGACCCTGGCCGCAGTGACGCCCAGAACCGTCCACCTCACCTGGCAGCCCTCGGCCGGGGCCACCCACTACCTGGTGCGATGTTCTCCTGCTTCCCCCAAGGGTGAAGAGGAGGAGCGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.341 A=NA C2=0.469
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.8=79.5)
A:
NA
C2:
PF0004116=fn3=PU(56.2=91.8)
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:
GTGGTGGTGGAGGGACCC
R:
CTCCTCCTCTTCACCCTTGGG
Band lengths:
270-1153
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development