HsaINT0037725 @ hg19
Intron Retention
Gene
ENSG00000188986 | COBRA1
Description
cofactor of BRCA1 [Source:HGNC Symbol;Acc:24324]
Coordinates
chr9:140158697-140160431:+
Coord C1 exon
chr9:140158697-140158809
Coord A exon
chr9:140158810-140160328
Coord C2 exon
chr9:140160329-140160431
Length
1519 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
TTCACCTGGTGCCTGGACGCCTGCATCCGAGAGCGGTTCGTGGACAGCAAGAGGGCGCGGGAGCTGCAGGGGTTTCTCGATGGCGTCAAGAAGGGCCAGGAGCAGGTGCTGGG
Seq A exon
GTGAGGGTCGGCTCCACGAGGCCTCTGCCCCTCAGGGCCCTGCGTGCATCCGGTCTGCGCTTGCTGTGTTTTGCCGTGGGTAGCAGGCGTTTATTCCCGGATATTGCTTTTTCTTTTGTTTTTTTCGAGACAGAGTCTCGTTCTGTAGCCCAGGATGGAGTGCAGTGGTGCAATCTCTGCTCACTGCAACCTCCGCCTCCTAGGCTTAAGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCACGCGCCACTGCGCTCAGGTAATTTTTGTATTTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTTGTCTTGAACTCCTGACCTCAGGTGATCCACCCGCCTCAGCCTTCCAAAGTGCTGGGATTACAGGCATGCGCCACCGTGCCTGGCCTCCTGGATGTTTCAATAGAGCTATGCCGGGCACTGCTGGCCCACAGCTTAGGGACATGGTTGTCGGGATGTGTGTGGGTAGCAAAGTCTCCCTCCTCAACTCTGCATTCTGGAGCCAGGCCCAGGGGCTGGGGTCTGGTGTCTGCAGTGGCGTGGGGTCAGCCTCTGAGCTGAGGGGCATCCATTGGCATTTGCTTTCCAGCATCCTCTGGCTGGTGTATAGACACAGTGCTGCCTGGCCCTGCCTTTGCCACTTTTTTTCTTCCTTTTTTTTTTTTTTTTTTTTTTTCTGAGACAGGGTCTCTGTCACCCAGGCTTTAGTGCAGTGGTACAGTCTCCCTCAACCTCCTGGGCATTGATCCTGCTGTCTCCGCCTCCCAAAGTGCTGGGATTACAGGCACACACCAGTGCGCCTGGCCGATTTTTGTTATCTTTAGTAGAGATGGGATTTCACCACCTCGCCCGGGCTAGTCTCAAACAAACAATCCACCGGCCTCAGCATCCCAAAGTGCTGGGATGACAGGCGTGAGCCACCACACCCAGCCTTTTTTTTGTTTGTTTTTTTAACTTTTTAATTTGAAAAATCTTTGAATAGGTTAAGGACAAATTGCAAACCTTAAGCTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCGCTCTCTTGCCCAGGCTGGAGTGCAGTGACGCGATCCTGGCTCACTGCAAGCTCTGCCTCCCGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACCACAGGCGACCACCACCACGCCCGGCTAATTTTTTGTATTTTTGGTAGAGACAGGGTTTCACTTTGTTAGCCAGGCTGGTCTCAGTCTCCTGACCTGGTGATCCATCCGCCTCGGCCTGCCAAAGTGCTGGGATGACAGGCTGAGCCGCCGCGCCCGGCCTGCCAAAGTGCTGGGATGACAGGCTGAGCCGCCGCGCTCGGCCATCCTTAAGCTTTTTGTAAGAAACCCAGCATGTGATGGGCACCCGCTGCCAGTCCTGAATTCAGCCTAGGCCACCCCTCCTGAGGACTGTGCCGCTGAAGGGAGGGGCAACAGGCGTCGCATTAATGCCAGGGCGGCCTCCTTCCAG
Seq C2 exon
GGACCTGTCCATGATCCTGTGTGACCCCTTCGCCATCAACACGCTGGCACTGAGCACAGTCAGGCACCTGCAGGAGCTGGTCGGCCAGGAGACACTGCCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188986-COBRA1:NM_015456:6
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:
PF062098=COBRA1=FE(7.8=100)
A:
NA
C2:
PF062098=COBRA1=FE(7.2=100)
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:
TTCACCTGGTGCCTGGACG
R:
CCTGGGCAGTGTCTCCTGG
Band lengths:
216-1735
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)