MmuINT0024314 @ mm10
Intron Retention
Gene
ENSMUSG00000004892 | Bcan
Description
brevican [Source:MGI Symbol;Acc:MGI:1096385]
Coordinates
chr3:87996539-87997356:-
Coord C1 exon
chr3:87996985-87997356
Coord A exon
chr3:87996714-87996984
Coord C2 exon
chr3:87996539-87996713
Length
271 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
GAGTTATTTCTTCTCCGCAGGGG
3' ss Score
9.7
Exon sequences
Seq C1 exon
AGGATCGAGCCTTCCGCGTGCGCATCGGTGCCACGCAGCTGCGGGGCGTGCTGGGCGGTGCCCTGGCCATCCCATGCCACGTCCACCACCTGCGGCCGCCGCACAGTCGCCGGGCCGCGCCGGGTTTTCCCCGGGTCAAGTGGACCTTCCTGTCCGGGGACCGGGAGGTAGAGGTACTGGTGGCTCGTGGGCTGCGCGTCAAGGTAAACGAAGCCTACCGGTTCCGCGTGGCGCTGCCTGCCTACCCCGCATCGCTCACGGATGTGTCTCTAGTATTGAGCGAACTGCGGCCCAATGATTCCGGGGTCTATCGCTGCGAGGTCCAGCACGGTATCGACGACAGCAGTGATGCTGTGGAGGTCAAGGTCAAAG
Seq A exon
GTGAGAGGAGAGTGAGATCCCTAGAGAAAGGGAGGAAAGGACTCAGGCCCCCCTCCCCCCGCAAGGAGTTGATTGTGAGGCGGCTTAGCAAACCCTGCAGGGGAAAGGCACAGGGTGAATAGGGGGCCAGAGATGTGGGGGGAGACAGTCCCACAAGCTGTAACAGGAGCACAATCGGACTTTAACTTTTGTGAACAGGAAGTGACAGAAGAGAGGGGGAGGTCAGTGTGCTGGTGGTCCGGCCAACTCAGGAGTTATTTCTTCTCCGCAG
Seq C2 exon
GGGTCGTCTTCCTCTACAGAGAGGGCTCTGCGCGCTATGCTTTCTCCTTTGCTGGAGCCCAGGAAGCCTGCGCTCGCATAGGAGCCCGAATCGCCACCCCGGAGCAGCTCTATGCTGCCTACCTCGGCGGCTATGAGCAGTGTGATGCAGGCTGGCTGTCCGACCAAACTGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004892:ENSMUST00000090971:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.009 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0768612=V-set=PD(87.9=98.4),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=PU(60.4=98.3)
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:
CATCGCTCACGGATGTGTCTC
R:
CTCACAGTTTGGTCGGACAGC
Band lengths:
298-569
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types