HsaALTD0001524-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000188986 | COBRA1
Description
cofactor of BRCA1 [Source:HGNC Symbol;Acc:24324]
Coordinates
chr9:140158697-140160431:+
Coord C1 exon
chr9:140158697-140158801
Coord A exon
chr9:140158802-140158809
Coord C2 exon
chr9:140160329-140160431
Length
8 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGG
5' ss Score
5.5
3' ss Seq
CCAGGGCGGCCTCCTTCCAGGGA
3' ss Score
6.14
Exon sequences
Seq C1 exon
TTCACCTGGTGCCTGGACGCCTGCATCCGAGAGCGGTTCGTGGACAGCAAGAGGGCGCGGGAGCTGCAGGGGTTTCTCGATGGCGTCAAGAAGGGCCAGGAGCAG
Seq A exon
GTGCTGGG
Seq C2 exon
GGACCTGTCCATGATCCTGTGTGACCCCTTCGCCATCAACACGCTGGCACTGAGCACAGTCAGGCACCTGCAGGAGCTGGTCGGCCAGGAGACACTGCCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188986-5-5,6-5-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF062098=COBRA1=FE(7.8=100)
A:
NA
C2:
PF062098=COBRA1=FE(7.2=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCGTGGACAGCAAGAGGG
R:
GGGGTCACACAGGATCATGGA
Band lengths:
98-106
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)