HsaALTD0001547-2/2 @ hg38
Alternative 5'ss
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63328079-63328498:+
Coord C1 exon
chr20:63328079-63328127
Coord A exon
chr20:63328128-63328145
Coord C2 exon
chr20:63328331-63328498
Length
18 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
GACACCCCTCCTCCCCACAGCAC
3' ss Score
9.96
Exon sequences
Seq C1 exon
GGCGAGCCGCAGTCCCTTGCCACCCTCTACCAGCTTGTGAGCCAGGCCT
Seq A exon
GTGAGTCTGCCATTCAGA
Seq C2 exon
CACACGTGTCAAAGTTCGACTCCTTCCACGAGAACACCAGGCCCCCCATGCCCATCTTGGAGCAGAAGCTGGAGCCGGGCACTGAGCCCCTGGGGTCCCCTGGCACCCGCAGCAAGGCCCTGGTTCCTGGAGAATGGGGGCGTGGTGGCCGCCACCTTGAGGGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-43-54,44-54-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.845 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(5.9=23.5)
A:
NA
C2:
NO
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
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:
AGTCCCTTGCCACCCTCTAC
R:
TTCTGCTCCAAGATGGGCATG
Band lengths:
106-124
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