HsaALTA1053498-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000196739 | COL27A1
Description
collagen type XXVII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:22986]
Coordinates
chr9:114288914-114289295:+
Coord C1 exon
chr9:114288914-114288967
Coord A exon
chr9:114289172-114289241
Coord C2 exon
chr9:114289242-114289295
Length
70 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
CCCCACCCCTCCCCCTCCAGGCG
3' ss Score
10.78
Exon sequences
Seq C1 exon
GGACAGGAGGGTGTGCAAGGCCTCCGTGGAAAGCCAGGCCAGCAGGGCCAACCC
Seq A exon
GCGGAGACTGGCCACCCTCCCCGGGAGAGAATCCTGGGGCTGCCTTGCGTCATCTCACCTTGGTTTGCAG
Seq C2 exon
GGGCATCCGGGACCCCGGGGGTGGCCGGGACCCAAAGGATCGAAAGGCGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196739-84-89,84-88-2/2
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=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.4=100),PF0139113=Collagen=PU(2.6=11.1)
A:
NA
C2:
PF0139113=Collagen=PD(22.6=77.8),PF0139113=Collagen=FE(22.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAGGAGGGTGTGCAAGG
R:
CTCTGCGCCTTTCGATCCTTT
Band lengths:
107-177
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains