HsaINT0038487 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61953410-61956846:+
Coord C1 exon
chr20:61953410-61953463
Coord A exon
chr20:61953464-61956792
Coord C2 exon
chr20:61956793-61956846
Length
3329 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
AGCCCATCTTCCCCCTCCAGGGT
3' ss Score
9.58
Exon sequences
Seq C1 exon
GGCCTCCCTGGGAGGAATGGCACCCCAGGAGAGCAGGGCTTCCCAGGGCCCAGG
Seq A exon
GTAAGTTTTGGGGAGCCCTGGGAGGTGAGGGGCCTGGATCGTACCTACCAGAAGAGAACACCCCTCCCAGTGCATTCCTGAGAGTGCAGGGAGCTGCACGCAGCTTCCCTAGGCAGGGTGGGGTCTCCCCAAGCTGCAGACAGGCAGGGACCCCAGCACCCCAGGAGTCCAGGGGGTTTAGGCTGGCCTCCCCCATGTGCCTGCAGGGCGCCTGGCCCAGGCCTGGTTATGGTGCAAGTCCCCTTTTCACCCAGATAGGGAGGATGAACCCCATGGCCCAGCAGGGGAATCTGAGGCTTGGGGAGGTGAGGCCACCTGTCCTATTGGCCCTGAAGGCCGCCCTTGATTTCCATGGGGCAGGCATGAGCCAGATGCCTTCTGTGTGCCGGGCTGGGCCCAGGAGCTTAGGCCCACAGAGTATTTTCAGATGTCTCTAGGCTCAGCGCATGCGCGGCGTGCAGGGAGGTGTTTCGGGGGCGGAGGTTCTGGTTCTGCGGAGAGGGATGTTGAAGACAGCGCGCCCAGCGATGGCAGCAGCCCCCCACCCCAGGCGCCAAAGGGCCGCCCTCCAGGCTCGATTCTAAACATTTACCTAAACCACGGTACTGCACAAGCGTGACACAGATGCCGAAGGCGTGGTCGGCATGCAGCAAGGCCGCCCTCCTCCCGACCCCGACACCCACCTCTCCCCCGGCAGCCTTCCAGCGAGTTCCACATCCCCGTGAGCAAAGACGTGCGCCTGGCTCTGGCGGGGCTGTCCTTTTGCACCTGCGCTGCCATATTCCCTTTGTCTGCGGTTGTGCTGGAGCCTCAGAGCACATCTCAGGCACAGAGTCCCTAGGACAGTCGCTGGGTGGAAGGGCACACGCCCCTGTGCTTTGGGGTGGATGTCCCCACACTGGCCCGGCAGAGCCGTGCGAGGCGCTCCCCCGCGACGAGCCAGCGGTGACCTCCCACCCCCATCTTGCATTCCTGGCTGCTTTGGGAGCCGCGTCTGATAGATGAAAATGCATTTCTCTTCCAAGCAGCGTGAATGCCCTTTGAAAGTTGCCAATATTTTCTTGCTGGAGATGTCCTCTGACTTCTTCTCCACCGTTCTTTTTTCTTAATAATTTGTGGGCACGCTTTTTACTTGCTGGAACCAGCCCTGTGTCTGTGATGTGAGTTTTGACTGCGTTTGGCATTTTCTTGTCTTTTGACCTTGTTTGCGACGTGCGTTTCCATACAGATTTTAAAATAACTTTTACGTAGTCCATGTTACTGCTCTGTTCTATGGCTTCTGAATTTTGTATCCTGTTTTAAAAGATCTTTCTTATTCCGAGAGTAGAAATCGCGCCTCCTCCTGGTTCCTCCTGGTGCTTCCAGGCACTTTTCGACACTCCCAGGTGGATTCGTCTAGAGCTGATTTTGTTACAGCACTGGGGAGGACAGAGGACGGGGAGGACTCCAGCTTCACCTCTTCACAGACCACCCCTGGTCGCCTGAGTCGTTCATTACACAGCCAGCCCCTTGCAGAAGTTGAACGCCCTGGCTCTCGTGCTGTCCTAAGGCCCCTGTGTATTTTGGGGTTTTTCAGATGCTCCAGTCTGTCCCGTTGATGTGTCTGTTGTTCACAGGCGAGGGCTGTGCTGCTTAAATTATTACAGATTTCTTTAAGATGTCGATGCCAGATGGGCTGGTCCTCTTTTGTATTATTCCCCCAGAATTTTCCTGGCTCTCTTTGCTTATTTCATTGTTCAGTGAACTGTAGAATCGACTTATCCGTTTAACCTAAACAATTCAGTTGGTGTTTTTACTGGAACTGCATTCGCTTTATAGATATACTCGGGAACAGATGATGTCTTCATGATGTTGAATCTTCTCATCCAAAAACACAGCCATCCTGCCTTTTGTTCACAGGGCCTGTTGTGGCCCTCAGTACAGTGTGGGGATGGTCTCTTCCTACAGACCCACTCGGTTCTCCTTCATCCCTACGTATGTCCTCTTTTTTGTTGCTATTATAAGTGAGGTGTTTTCTCTCATTACAGCTTCTACCTCATTATTTTCACACTGGCCGTGACCGCTGTGTATGACTTTTGTACCCAGTTTTCTTTCTCAATTATCTTCTTTGTGGTTTTCTTGGATTTTCCAGGTTTACAGTGACATCACCTGCAAATAAACACTTCACCTTCGGCTTTTCAGTCTTGATCACTCAAATTTCTTTTTCTTGTCTAATGGTGTTGGTGAATACTCCAGAATTTTGTCAGAGAACAGTGGCAGTAGCAGATACTCTCATTTTCTTCTTGGCCTAACAGAAGTGCTTCTAGCATTTGACCATTAAAGTGCTGTCCTGGAAGCGGAGACAGGTGCATTTTGTCATGTGGTAGTGAAGTCCATCCACTCTTCTTTTATTAGATTTAAAACACCAAGAATGCACATTAAACAAGCTCTAGTGCTGTTATGGACATAATGAAATGACTGTGCGTCTTGGAGCTATTAATTGTAGGATATCCCTAAATACTGGATGATTGCTGCATCCGTCGAAAATCTGACGTGGTCGCTGAATTCTCGTTATCCATGCCATGTGCTGCAGAGCTCAGCTTGCTGACATTTTGTTTTGGATTTCGCACTGATGCTTCTAAATAAGACTGTCACAGTTTTCTTTATAGTGTTTGGAACCTCAGTTTGCTTTGTTCAAAAGATAATTTGAGTTTAAATAGCAGCAGTGTCCTCTGCCCCACAGGGTTGGATTTCCCATAAAACCTGAGTCTAGTGTTTTGGGGTCCAGGGCTTAAGAAAGTTTTCTGTCTCTTCCATACAGTTGGCCTGTGGGGGTCTCTGGCTTTTCCTCGGTGATTTCTGCAGCGCCCCCCACACCCCGTTAGAACCCAGAGTTGGGCAGGGGAGGGCTGGGGGTGAGGTTGGTTGGAACTGGCTTCACAGGCTTGGCTCTGCCATTCTCTAGCTCTGCAGACCCCTGCTGTGGGTTCTCCCAGACCCTCCCAGGGTGAGCAGTGAGGGTGCTGGGGCTGCCCCTGCTCCTTTAATGGAGGTGTCTCCATGTCGGTCTGGGTCTGAATGCCCAGAGGGCTGGGAGGGCTGGCTGTGACCCAGAGGGGCCACAGGAGGGGTGGCAAGCGTGACCTTGTCAGGCCCTACCCGCTGCCTGTGTCTCCAGGGAGAGCCCGGGCCACCCGGACAGATGGGACCAGAAGGTCCTGGAGGCCAGCAGGGCTCGCCGGGGACCCAGGGCCGTGCAGTCCAGGGGCCTGTGGTAGGTGTCACTCCTTCCCTGCCCTCCTGCCCTGTGCCCCCTCCGCTTCGCTGTCCAGCCCATCTTCCCCCTCCAG
Seq C2 exon
GGTCCACCAGGGGTCAAAGGAGAGAAGGGAGACCATGGGCTTCCAGGCTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:27
Average complexity
IR-S
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=FE(28.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(29.3=100)
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)