HsaALTD1005570-2/2 @ hg38
Alternative 5'ss
Gene
ENSG00000084636 | COL16A1
Description
collagen type XVI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr1:31694144-31695221:-
Coord C1 exon
chr1:31695186-31695221
Coord A exon
chr1:31695103-31695185
Coord C2 exon
chr1:31694144-31694170
Length
83 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
CCTCTCCTCTGTCCCCTCAGGTC
3' ss Score
13.22
Exon sequences
Seq C1 exon
TGTCCGCCCTGTGTCCATGGTGCCCGGGACAGCAAT
Seq A exon
GTGAGTGAATGGAGGGTGTGCAGGGTGGAGCGGGCAAGAGCCGGGAGTGGACGTTGCCTAGAGCTGGCTTGGCAGCCTCCTGG
Seq C2 exon
GTCACACTTGCTCCCTCTGGCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636-19-18,20-18-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.811 A=NA C2=0.909
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(15.9=58.3)
A:
NA
C2:
PF0139113=Collagen=FE(18.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
TGTCCGCCCTGTGTCCAT
R:
CTTGGGGCCAGAGGGAGC
Band lengths:
63-146
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains