HsaALTD1041805-2/2 @ hg38
Alternative 5'ss
Gene
ENSG00000196739 | COL27A1
Description
collagen type XXVII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:22986]
Coordinates
chr9:114210982-114219844:+
Coord C1 exon
chr9:114210982-114211018
Coord A exon
chr9:114211019-114211026
Coord C2 exon
chr9:114219791-114219844
Length
8 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAAG
5' ss Score
6.84
3' ss Seq
TTCTCTCTCATGCCCTCCAGGGG
3' ss Score
9.84
Exon sequences
Seq C1 exon
GGCCTGCCTGGCGTTCCTGGCAAGAGGGGCAAGATGG
Seq A exon
GTATGCCG
Seq C2 exon
GGGTTTCCTGGAGTCTTTGGGGAAAGAGGCCCTCCTGGACTGGATGGAAATCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196739-22-24,23-24-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(9.1=46.7),PF0139113=Collagen=FE(20.3=100),PF0139113=Collagen=FE(16.5=100)
A:
NA
C2:
PF0139113=Collagen=PD(15.9=61.1),PF0139113=Collagen=FE(20.0=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCGTTCCTGGCAAGAG
R:
GATTTCCATCCAGTCCAGGAGG
Band lengths:
82-90
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains