HsaINT0037717 @ hg19
Intron Retention
Gene
ENSG00000188986 | COBRA1
Description
cofactor of BRCA1 [Source:HGNC Symbol;Acc:24324]
Coordinates
chr9:140149759-140150522:+
Coord C1 exon
chr9:140149759-140150063
Coord A exon
chr9:140150064-140150358
Coord C2 exon
chr9:140150359-140150522
Length
295 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
GTTTCTCTTGGCTTCCTCAGACA
3' ss Score
7.79
Exon sequences
Seq C1 exon
GGTGCGGGGCGGAAGTGGGCGGCTGCGGGACGCGCGCGGAGTCGCGCGGCGGGCGGGACCTGGCCGAGCTGGAGGGCGCCGGGGAGCGGGGCTCGGGCGGTCCCCGAGGCCCGGCGGAGCGGGCTTCTGGGGTGTCTGCGGCGGCGCCGGGGGAACGGGCTGGGGATGGGGCGCCTAGCCGGGCGGTGGCCGGGGCCTCGGCCATGTTCGCGGGGCTGCAGGACCTGGGCGTGGCCAACGGCGAGGACCTGAAGGAGACCCTGACCAACTGCACGGAGCCGCTCAAGGCCATCGAGCAGTTCCAG
Seq A exon
GTGGGGCGGCCCCCGGGGCGGGGGGAGCCCAGTTGGAGGGCCGGGCCGCCTGCTCGGGAGTCGGGCCTGGCGGAGGCGCCGGAAGTTTTCCGGCTTTCTGCTGGTGGCTGAGTCCTGTTCTGGGGGTGGAGTCCGGAGCCAGCACCCCTTTGCTGGACGGCTGGGTGGCTTTCGGTGGCTGCGGTTACCGCCAGCACGGCTGGGAACACCTGGGTGCGTGCCTCCCTGTGCTCTCAGGACCTCGGGGTGCCCGGGCGCACTGGGCTGCGTTTGAGGTTTCTCTTGGCTTCCTCAG
Seq C2 exon
ACAGAGAATGGTGTGCTGCTGCCATCTCTTCAGTCAGCCCTCCCCTTCTTGGACCTGCACGGGACGCCGCGGCTGGAGTTCCACCAGTCGGTATTCGATGAGCTGCGGGACAAGCTGCTGGAGCGAGTGTCAGCCATCGCTTCGGAGGGGAAGGCTGAGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188986-COBRA1:NM_015456:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTCTGGGGTGTCTGCG
R:
GTCCCGCAGCTCATCGAATAC
Band lengths:
294-589
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)