MmuINT0038664 @ mm9
Intron Retention
Gene
ENSMUSG00000013465 | Cobra1
Description
cofactor of BRCA1 [Source:MGI Symbol;Acc:MGI:1931035]
Coordinates
chr2:25058868-25059502:-
Coord C1 exon
chr2:25059407-25059502
Coord A exon
chr2:25059011-25059406
Coord C2 exon
chr2:25058868-25059010
Length
396 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGA
5' ss Score
6.56
3' ss Seq
TCAGACACTCCTTCTGCCAGGAG
3' ss Score
4.69
Exon sequences
Seq C1 exon
GATAGTCCCGACCTCCTCCTACTACTTAGGCTGCTGGCACTGGGCCAAGGTGCATGGGACTTAATAGATAGCCAGGTCTTCAAGGAGCCTAAGATG
Seq A exon
GTATGAGGTCTGGTTTCCTCCTTTTCTTTTAATTATGGGGAGTGGAAGGGTGGGGGCCCTCTGGTAGGAAAACTCTACTCCTAGAACACCTATGAAGGATGTTTGGGTATCTTGGTGAACTGGCTGCAGGGTGGAGCTAGTCCATGGGGACTGGGGTTCAGATGGGGCTTTGCAGGTGCAGCCATGATGGAGGATTCAAGAATATAGCACTCAACATGAGTCTCAGGAAACAGGGAGGAGGGGTTCGGGGAGGGGGACAATGTCCAGGAAAGCTGGATTTGAGACAAGTGTATTAGGGGTAAGGGCAAGGTGTACATGACAGAGTAGGTTAGGGTGTCTATTGAGAGCAGCCAGGCTCAGGGGGACCTTAGTGGACTCAGACACTCCTTCTGCCAG
Seq C2 exon
GAGGCAGAGCTCATCACCAAGTTCCTGCCGATGCTCATGTCCCTCGTGGTGGATGACTTCACTTTCAACGTAGATCAGAAGCTTCCAGCTGAGGAGAAAGCCTCAGTCACATACCCCAACACACTTCCTGAGAGTTTCACCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000013465-Cobra1:NM_021393:8
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=PU(7.6=91.7)
A:
NA
C2:
PF062098=COBRA1=FE(15.3=100)
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:
GATAGTCCCGACCTCCTCCTAC
R:
TGGTGAAACTCTCAGGAAGTGTG
Band lengths:
238-634
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: