MmuINT0038658 @ mm9
Intron Retention
Gene
ENSMUSG00000013465 | Cobra1
Description
cofactor of BRCA1 [Source:MGI Symbol;Acc:MGI:1931035]
Coordinates
chr2:25065958-25066392:-
Coord C1 exon
chr2:25066229-25066392
Coord A exon
chr2:25066058-25066228
Coord C2 exon
chr2:25065958-25066057
Length
171 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
AGCTGTGCAAATCTGTGCAGGTA
3' ss Score
5.74
Exon sequences
Seq C1 exon
ACAGAGAATGGCGTGTTGCTGCCTTCCCTGCAGTCGGCCCTGCCCTTCTTGGATCTACACGGGACACCGCGGCTGGAGTTCCATCAGTCAGTGTTTGATGAACTACGTGACAAACTTCTGGAACGAGTGTCAGCAATTGCCTCTGAGGGAAAGGCAGAGGAGAG
Seq A exon
GTGGGTCTCTACCAGGAAGCTGCTTATCTTTGTGAGTAGCATTGATGGTCTCCATGGCTGCACAGCCCTACCTGTAGATACAACCTGGAATGGAATGTGTTTGAGGGATTCCTCTTCTCTGTATGTTCTGCATGTGGAGACACACTTCCTCAGCTGTGCAAATCTGTGCAG
Seq C2 exon
GTACAAGAAGCTGGAAGACCTTCTGGAAAAGAGCTTTTCTTTGGTCAAGATGCCATCCCTACAACCAGTGGTGATGTGTGTTATGAAACACTTGCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000013465-Cobra1:NM_021393:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
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(84.2=47.1),PF062098=COBRA1=PU(0.6=2.9)
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:
ACAGAGAATGGCGTGTTGCTG
R:
ACACACATCACCACTGGTTGT
Band lengths:
245-416
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: