MmuINT0024313 @ mm9
Intron Retention
Gene
ENSMUSG00000004892 | Bcan
Description
brevican [Source:MGI Symbol;Acc:MGI:1096385]
Coordinates
chr3:87800907-87801777:-
Coord C1 exon
chr3:87801667-87801777
Coord A exon
chr3:87801279-87801666
Coord C2 exon
chr3:87800907-87801278
Length
388 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
GCTTTGACCCCTGTCCACAGAGG
3' ss Score
8.36
Exon sequences
Seq C1 exon
TTCTTCCATCAGTGTGCAGAATGATTCCACTGCTTCTGTCCCTGCTGGCCGCTCTGGTCCTGACCCAAGCCCCTGCCGCCCTCGCTGATGACCTGAAAGAAGACAGCTCGG
Seq A exon
GTGAGTAAGCATCCAGAGGACCATGTCTCTGCTGCATCTTTCTCAGGACAGAGGGCTGTCTCGGTTTAGCCCCAGCTACATGCTTCCAGCCTAGGCACACGGAAGGAGATGTGGAAGTGCTGTGGGCAAGGGCTGGAGCCAACTGCAAAATAGGGATGAATTGGGAACCCTAGTAAGTAGGGGAGTCTTGGGGGTCAGAGTTGCAAAGGAGCACGAGGCAGGAGGCTAAGGGTAGAGGATCAAATTCAGGACCCTGGGCAGTGCTCAGCACCCTGAGCTGGGCAGTGCACCCCAGGCGCCTTGGATCGAGGGGCGGGGCTTGGAGCCAAGCGCACAGGCGCACTACGTCCTGCGTCTGGCTGCAGCCGGCTTTGACCCCTGTCCACAG
Seq C2 exon
AGGATCGAGCCTTCCGCGTGCGCATCGGTGCCACGCAGCTGCGGGGCGTGCTGGGCGGTGCCCTGGCCATCCCATGCCACGTCCACCACCTGCGGCCGCCGCACAGTCGCCGGGCCGCGCCGGGTTTTCCCCGGGTCAAGTGGACCTTCCTGTCCGGGGACCGGGAGGTAGAGGTACTGGTGGCTCGTGGGCTGCGCGTCAAGGTAAACGAAGCCTACCGGTTCCGCGTGGCGCTGCCTGCCTACCCCGCATCGCTCACGGATGTGTCTCTAGTATTGAGCGAACTGCGGCCCAATGATTCCGGGGTCTATCGCTGCGAGGTCCAGCACGGTATCGACGACAGCAGTGATGCTGTGGAGGTCAAGGTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004892-Bcan:NM_001109758:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.008
Domain overlap (PFAM):
C1:
PF0768612=V-set=PU(11.4=51.6)
A:
NA
C2:
PF0768612=V-set=PD(87.9=98.4),PF073547=Sp38=PU(56.0=33.6),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:
CCCTCGCTGATGACCTGAAAG
R:
AGCGATAGACCCCGGAATCAT
Band lengths:
348-736
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: