HsaINT0037721 @ hg19
Intron Retention
Gene
ENSG00000188986 | COBRA1
Description
cofactor of BRCA1 [Source:HGNC Symbol;Acc:24324]
Coordinates
chr9:140150359-140150880:+
Coord C1 exon
chr9:140150359-140150522
Coord A exon
chr9:140150523-140150780
Coord C2 exon
chr9:140150781-140150880
Length
258 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
AATCCTGTGAGTTGTTCCAGGTA
3' ss Score
2.3
Exon sequences
Seq C1 exon
ACAGAGAATGGTGTGCTGCTGCCATCTCTTCAGTCAGCCCTCCCCTTCTTGGACCTGCACGGGACGCCGCGGCTGGAGTTCCACCAGTCGGTATTCGATGAGCTGCGGGACAAGCTGCTGGAGCGAGTGTCAGCCATCGCTTCGGAGGGGAAGGCTGAGGAAAG
Seq A exon
GTGGGTCAGCGGGAGGGGTGGGCAGGTGAGATGTGCAGCCGGCCTCTCAGCCTTGGATCGACTCAGGGGCATTTATTGTCCTTTTGGCTCCACATCCTTGCTCCCAGAGGTGGCCTGGGCCTGTGTCTGAGTGACCCCTTGACCCATGTGTCCTGGGCGTGGAGGCTTGTCCTGGTAGCTGTTATCTGTGTAGGGACAGGCAGGTAGCTGCTGCGATTTGGCGCATCGCTGCACCATCAATCCTGTGAGTTGTTCCAG
Seq C2 exon
GTACAAGAAGCTGGAAGACCTTCTGGAGAAGAGCTTTTCTCTGGTGAAGATGCCGTCCCTGCAGCCCGTGGTGATGTGCGTCATGAAGCACCTGCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188986-COBRA1:NM_015456:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF062098=COBRA1=PU(3.4=47.1)
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:
ACAGAGAATGGTGTGCTGCTG
R:
CTTGGGCAGGTGCTTCATGAC
Band lengths:
264-522
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)