HsaINT0038479 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63295040-63298020:+
Coord C1 exon
chr20:63295040-63295189
Coord A exon
chr20:63295190-63297909
Coord C2 exon
chr20:63297910-63298020
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
GTCAGGGAGAGGACAGACGGGGGGACGGCTGAAGGGCATGGCCTCTTCCCTGCCACAGCCCGAGCACCATGAGCTCCGGAGACCCTGCACACCTCGGCCTCTGCCTCTGGCTGTGGCTGGGCGCCACCCTGGGAAGAGAGCAAGTTCAAG
Seq A exon
GTAAGGACACTGGCAGTGGGCCCCTGCTTGCCCCGAGGCCACGCCTGCCCCACCAGTGCCCACGCGGGACGAGCCCTCCGCCCCTGAGCCCCGTCTTCCTCCTAAGTTGAATGCGTGCTGAATTCACAGCAGCTCCCACAACAAAGGCAAGACGGGAGGGAGCGTGTGCTCCCGCCAAACCTTCAGCCTCGCCTTGGGAGCACATCTCTGTGGTTTAGTTCTCTGTTATATTAATGCTTGGCCGAGAGTTATTCCACGAACACCTTTCGGAGCAGTCTCTAGGAAGCAGGAGGCTGGGGTAAAGATGGAGCCGCCTTCCCTTCCCTCCTGCCTGCTTCCCACCGCCGCCTCCCACTGGTGTTTTGGGCACATAGCCCTCTGGCTTCTCTCGGTGCGGCACTCGCATTTCCACGCAGCACCACCCCCTCCGTGCGCATCCCTGGGCGACAGCACCACGTCCTCAGAAGGCCCCTCCAGTCTGGCTGCTACTGGTTGGGGCGTTTGGGTAACGTAGGGCACCGCCCATGGCAGCAAAGGGAAATGGCAGAGGATGCTGTGGGCTCACCTGTCTGAGCAGCTTCTTCCTCCTGTTGAGAAATGTGGGTTTAGATTGACTCTAGGAAGGTGAATTTCCGTGTCTATGGAGAAGGCTCCGGGGCCTCGGCCACGCTGTAAACTTGTCCCTGGGCTGGGCCAACGCGGCGCCTCCCGGCACCTGCAAGCTCCTGGGAGGTTCCGGGCTCCCACTGAGCGATGGTTTTGTTCCGCTGGGGTGAAAGGCAGCTCCCCCTTCTACTGTGCGTTTAAAGCACCCCCACCAGGGCCTGACAGGCCGGGGCGAGGGAGCCTCCAGGTGCCGCTGCCATTGCAGAAGGGCGGGTGAGATGCGGGAGCCCCGGTGTAGCGTGGAGCCGCCTGTTGAGACCCTTCCGGGTTTCACGGCTTGTCTTGCCATGCTGATGTGCCAGGTTTGCCCTGCACACAGGCAACAGACCATTGCATGAGCAGGTGCCTTGGTCCCCTCAGCTCAGACAGGGTAACCCTGCCCTGGGGCCAGTGGGGGCTGAGATTTCAGTTTGAAAGAAGCTTGCACTGTCAATTTGAGCCAAATCAGTAAGTTGCTTCTACAGAAACAACTTGAGTTTAGGCGAAGGCAAATCTAGTTCTATCTAGTTCAGGATTCAGCATGATGGGGCCACCCCTCACAAGGGCCTTTCGGGGGCCATTGAGTCCCTGAGGACAGCCAGGTGGGCTGGGGGCACTGAGTCCAGCCCAGGACGGGTGGGAGCCCACACGCTGGGGCAGCCCTTCCCAGGATGGCCCAGGCTGGGTGCGGCCACAGTCCAGGGAGGGGAGCGTGGTCCTGGGTGGGGCCCTTCCCACCAGCCGCTGTCTGCCCAGTGCCCTGCTCAGGCCCCAACAGTGCTGTCCTCCAGCAGGGAGCTGGGGAAGGGGTCCCTGACGTTCTCAGGCAGAGTGGAGCAACAGAAGGCTCTTCACAAGCAGGGGCTGCGGGAGGGGCCCTGCTCACAGCTGGCCTTCAGAGCCCCCTCCTCATCCCCCACACATTCCTGCCTTTCAGCCCCATCCGGAGACCCGGCCCAGCTGCTGCCTGCTCTGAATGGGTCATTGTGTCTGCCCCAGTGCCCCCCAGCCCCTGCTCTTCCCCCCGAGCCCCAGCTTTCCGGGGGGCAGCCCAAAGAAGCCCATCTCTGTCCCCATTTTCCAAAAATAGCTGCCCCTACTGCAGAGCCCCGGAAGCTTTCAGGGGGCACCAACCCTCTCCAGAGCCCTGGGAGGTTGGCCAGGCCCCTGCCGCCCCCTCTTCCTCTCAGATGGCCTGGACACCCATCCCCCATCGCGGGAGGCAGCCTCGTCTTGGCATGGACGCACACATGTACCAACGTGCACACACGTGCCAATGTGCACACACTTCCAGTGTGGGATTCTGCACCCACACTCCCCACTGAGGCGGCACGTGCACCTGGCAGTGACCTTGGCAGCTAGGGGTCTGCAGCTGCATGGCCACTTGTCCTGGGGACCCAGCCCAGGGGACTCAGCCCAGGGGCCCCAGCCCAGGGGACTTAGCTCAGGGGACCCAGCCTGGGGACTCAGCCCAGGGGCCCCAGCTCAGGGGACTTAGCTCAGGGGACCCAGCCCAGGGGACCCAGCTCAGGGGACTCAGCTCAGGGGACCCAGCCCAGGGGACTCAGCCCAGGGGCCCCAGCCCAGGGGACTTAGCTCAGGGGACCCAGCCCGGGGACTCAGCCCAGGGGCCCCAGCTCAGGGGACTCAGCTCAGGGCCCTGGGCAGGTTGCCAGCTGCTGTGTTGGCTCGGGGCCTCCGATCATCAGTGGGGTGGTTGCTGTCCTCCCAGACATGGGCCTGAGCCTCTTCCTGGTGGGAGGACCCCCGGAGAGCCAGGCTGGGGCCTCCCTGGGTGGGACTGGACTCCCTCTCACCAAAGCTACCAGGGTGGCCCTGTGACTGCGGACCCCGGGGAGGGCCGGGTTCTCCTCAGCGCCCAGGCGAGGCCTCGTATCCCCAAGTGGGGCTGAGTCCGCCTCAGACACCCTGGGTGGGCTTCTGTCTCTTCGGGGTCCCCCGGGATAGGACTGTGTTCCTCCCAAATGCTGAGGGCAGGATGCCTGTACCCCCACAGCTGATTAGGTGGATGGGGAGGCCAGGTCAGTCCTGACCACTATGTCCTGTTTCTGTAG
Seq C2 exon
CAAGCGGTCTCCTGAGGCTGGCTGTGCTGCCTGAGGACCGGCTGCAGATGAAGTGGAGAGAGTCGGAGGGGAGCGGCCTCGGCTACCTGGTGCAGGTGAAGCCCATGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:1
Average complexity
IR
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
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