MmuINT0038662 @ mm9
Intron Retention
Gene
ENSMUSG00000013465 | Cobra1
Description
cofactor of BRCA1 [Source:MGI Symbol;Acc:MGI:1931035]
Coordinates
chr2:25059718-25060759:-
Coord C1 exon
chr2:25060647-25060759
Coord A exon
chr2:25059821-25060646
Coord C2 exon
chr2:25059718-25059820
Length
826 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGA
5' ss Score
4.74
3' ss Seq
CAAGGTCTGATTCCTTCCAGGGA
3' ss Score
6.87
Exon sequences
Seq C1 exon
TTCACCTGGTGCCTGGATGCCTGCATCCGGGAACGGTTTGTGGACAGCAAAAGAGCCCGGGAGCTTCAGGGATTTCTTGATGGTGTGAAGAAGGGCCAGGAACAAGTTTTGGG
Seq A exon
GTGAGAGCTCTTTGAGGACCCTAGCCTTTGATCCCTAAACAGGCATCGGTGGGGTTTGCTGTTCACCTTTGGTAGTTGGAGCCTATTCTGGTATGTTTGGGACAGTCATGCTTGGTACCAGGCCCACTGTTAACAGAGTGCTAACTCATTACTTGGAATGAGCCTTAGTAGCAGGAGGATCAATACCTGTGCATGGAGTTTGAGGCCTGCTGCTCGTGGGGCAGCCAGCACAGGGAGCTTAGTCAGGGAGGGGATTGTTGTTTATGGCAAGTTGGGTGTAAGCTGAGGGCTGGATTAGATACTCCAGCCTGATTCCCAGAATTCTTTGCCTGGCAGGAAGACATGCAGCTGCCACAGCCTTGCCACATTTCTCTGTTTTCTTCCACTGGCTAAACCTAGGGTTGAAGCCAGGCGTTTGTTTCTGTTTTGAGACAGGGCCTTAACTTTGTGGCCAAGCTGACATGAGATTCACTATGTAGACCAGGCTGACCCCAAACTCATTATGAGTTTCTCTCTCTCTCTCCCTCCTGAGTGCTAGAATTAAAGTCACATATCATTGCTTGCCCCTGAGTCAGGGTTTTTCAAGCAGTATGAATTTAGTATGCTGGGGTTTAATTTTTTTCTTTAACTTTGTAGTTTAGAAGATCTTTGAGTAAGTTATGGATAAATTATGAATTCAGTACAGAGAGAGGCTGGCTATCCGGGGTCAGTCCCCAAGCCCTTGCATCCCAGTCTGTGGCTGTCCCTTTAGTGGGTCTGGCACTGTAGCTATTAGAAACAGAGTAATCAGGCTTCTCAATTTATACCAAGGTCTGATTCCTTCCAG
Seq C2 exon
GGATTTGTCTATGATCCTGTGCGACCCCTTTGCCATCAACACACTGTCCCTGAGCACCATCAGGCACTTGCAGGAGCTGGTTAGCCAGGAGACACTGCCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000013465-Cobra1:NM_021393:6
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(22.3=100)
A:
NA
C2:
PF062098=COBRA1=FE(20.5=100),PF075846=BatA=PU(58.1=71.4)
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:
TTCACCTGGTGCCTGGATGC
R:
TGGGCAGTGTCTCCTGGCTA
Band lengths:
214-1040
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: