HsaALTA1011083-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63321013-63322111:+
Coord C1 exon
chr20:63321013-63321099
Coord A exon
chr20:63321728-63322057
Coord C2 exon
chr20:63322058-63322111
Length
330 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CTGCCTCTGCTCACCCCAAGGTT
3' ss Score
7.35
Exon sequences
Seq C1 exon
AGGGATGGAGAGACCTGCCCCGCCTTCGTGTCTGCCTGTTCCTGTTCCTCAGAGACCCCTGGGCCCCCAGGACCTCAAGGACCCCCA
Seq A exon
GTTCCAGCGCCCCACAGGTGACGGCTGGGGCTTCCAGAGCTGGCTCTGGGACCGGTCAAGCACACTCTCTCTGAGCTCAGTGTCCACAGCCTTGTCTACTCAGGGGGCCGGGGTTTGAACCCAGAACTGCCTGACTATGAGAGGGAAGGATGGGCTAGTGCGTCCTTGCCCTGGAAACCCCTTCTCTTCCCCTTGACAGCAGTGGACAGTCTGGGGCTGGGTGGGGCATGGGGCTCAGGGTGGGCCAGGCATGGGGCTCAGGGGCTGGTCTTTGCTCCTCTACCTTGGTTGGGTAGTTCTGGGGGCTTAGCCCTGTTTGTGCCTCTGCAG
Seq C2 exon
GGCCTCCCTGGGAGGAATGGCACCCCAGGAGAGCAGGGCTTCCCAGGGCCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-28-38,28-37-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.517 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(14.5=37.9)
A:
NA
C2:
PF0139113=Collagen=FE(22.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
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