MmuINT0024315 @ mm9
Intron Retention
Gene
ENSMUSG00000004892 | Bcan
Description
brevican [Source:MGI Symbol;Acc:MGI:1096385]
Coordinates
chr3:87800040-87800635:-
Coord C1 exon
chr3:87800461-87800635
Coord A exon
chr3:87800168-87800460
Coord C2 exon
chr3:87800040-87800167
Length
293 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
AGCCTCTTCCTCTCTCTTAGGTA
3' ss Score
9.5
Exon sequences
Seq C1 exon
GGGTCGTCTTCCTCTACAGAGAGGGCTCTGCGCGCTATGCTTTCTCCTTTGCTGGAGCCCAGGAAGCCTGCGCTCGCATAGGAGCCCGAATCGCCACCCCGGAGCAGCTCTATGCTGCCTACCTCGGCGGCTATGAGCAGTGTGATGCAGGCTGGCTGTCCGACCAAACTGTGAG
Seq A exon
GTGGGCTGGGGATGTAGACCAGGAACTCCTGGTCACATCGGGATGCTTGCTACCTCCTCCCTCCATCGAAGTTCCTCAGGATTCCCTGCCTCTGGAAAGAAAATTGGTCTGCAGCTCTGCCTGGGCCTTACTTTCCTGCATCCTGACATCACACACACACACACACACACACACACACACACACACACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGGGTTGACATGGGACAGCCTTCTGGGGTGGAAGATGCCAGGCATTAGCCTCTTCCTCTCTCTTAG
Seq C2 exon
GTACCCCATCCAGAACCCACGAGAGGCCTGCTCTGGAGACATGGATGGCTATCCTGGCGTGCGGAACTACGGAGTGGTGGGTCCTGATGATCTCTATGATGTCTACTGTTATGCCGAAGACCTAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004892-Bcan:NM_001109758:4
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:
PF073547=Sp38=PD(42.7=54.2),PF0019312=Xlink=PU(60.4=98.3)
A:
NA
C2:
PF0019312=Xlink=PD(38.5=84.1),PF0019312=Xlink=PU(0.1=0.0)
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:
GGGTCGTCTTCCTCTACAGAGA
R:
GGTCTTCGGCATAACAGTAGACA
Band lengths:
297-590
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: