MmuINT0038654 @ mm9
Intron Retention
Gene
ENSMUSG00000013465 | Cobra1
Description
cofactor of BRCA1 [Source:MGI Symbol;Acc:MGI:1931035]
Coordinates
chr2:25066229-25067009:-
Coord C1 exon
chr2:25066622-25067009
Coord A exon
chr2:25066393-25066621
Coord C2 exon
chr2:25066229-25066392
Length
229 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
TTTACCCTCTGCTTCTCCAGACA
3' ss Score
9.38
Exon sequences
Seq C1 exon
TGGGTAGCAAGTCGCTGCTCGGAACCTGCGGGCGGCGGAGGCGTTTTCCCGGGGCCTATTGGCTGCTGGACCTAGGCAGTCAAGGGCGGAAGTGGGAGGTGTGGGTCCGTGCGAGCTGCTCTGCTGACGCGATCTGGCCACACTGGAGGCGGCGGGCGAACGGGGCTTGGGGGGTCCTCGTGGCACCGTGGAGAGGGCTTCTGGGGCTCCGTCAGGGTCCGCTACGGCTCCAGCGGAGCGCGGTGGGGATGGGGTACACAGCCGAGCGTCCGCCGGAGCCTCCGCCATGTTCGCGGGGCTCCAGGACCTGGGCGTGGCCAATGGCGAGGACCTGAAAGAGACCCTGACCAACTGCACCGAGCCTCTCAAGGCCATTGAACAATTTCAG
Seq A exon
GTGGGCAGAAGGGGCCGGGGCAGCTAGGGAAGCTGGACACAATTCGGCGCGCTCCCGACGCTTGGATGGAGGCGCTAAAGGTTCTGCGCTAGGGACCCGCTGAGTAACTGAGTGTTTTCCCTTTTCCGCTGTTACTATGGCGGACCCTAGTACTCGGCATCCGTGGTGTCCGTGCTGACTTGGCTGCGGCCAAGCAAAATGCGTACGCGTTTACCCTCTGCTTCTCCAG
Seq C2 exon
ACAGAGAATGGCGTGTTGCTGCCTTCCCTGCAGTCGGCCCTGCCCTTCTTGGATCTACACGGGACACCGCGGCTGGAGTTCCATCAGTCAGTGTTTGATGAACTACGTGACAAACTTCTGGAACGAGTGTCAGCAATTGCCTCTGAGGGAAAGGCAGAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000013465-Cobra1:NM_021393:1
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGGGGATGGGGTACACAG
R:
CCCTCAGAGGCAATTGCTGAC
Band lengths:
296-525
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: