MmuINT0024321 @ mm10
Intron Retention
Gene
ENSMUSG00000004892 | Bcan
Description
brevican [Source:MGI Symbol;Acc:MGI:1096385]
Coordinates
chr3:87987531-87988462:-
Coord C1 exon
chr3:87988272-87988462
Coord A exon
chr3:87987968-87988271
Coord C2 exon
chr3:87987531-87987967
Length
304 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
GGTGTGTTTGTCTTCCATAGGGC
3' ss Score
10.8
Exon sequences
Seq C1 exon
TGTCCTGTGGGCCTCCACCACAGCTACCCCTGGCTCAAATATTTGGTCGCCCTCGGCTGCGCTACGCGGTGGATACTGTGCTTCGATATCGATGCCGAGACGGGCTGGCTCAGCGCAACCTGCCGTTGATCCGCTGCCAGGAGAATGGGCTTTGGGAGGCCCCTCAGATTTCCTGTGTACCCCGGAGGCCT
Seq A exon
GTAAGTGACAGGAGGAAACAGGTAGGGGGCACCAGCTACTTGGCAGCCCTAGGCTCAAAGACCCATTATGCCTGCCATTCACTGACTGAGCTTGGAGTGACCACTGCCTCTCGCTGAGGCTAAGAGAAGGAAATAGGCTGGAGCTCTGGAGACCTCGTGGGTGCAGATGGCTGAGAACCTGCAACCACACTTGGGCTCCTAAGGGCAGAGCAAGTATTTTGAAAAGGGCAGGGGTTAAGCAGCAATGACCCAGGTTATTAAGGAGGAGCGCCGTGCAGAGGATGGGTGTGTTTGTCTTCCATAG
Seq C2 exon
GGCCGTGCTCTGCGCTCCATGGACGCCCCAGAAGGACCACGGGGACAGCTCTCGAGGCACAGGAAGGCACCGTTGACACCGCCCTCCAGTCTCTAGGGAGCCTGGAAGACTGCTGCCCCCAGCAGGACCCTCTCACATCAACTGCCAGTGCTCTTCCCCATGATAGGGGGTGACGTGAGAGGGGTGGGACTGAAATTCAGAGGACAGCGCTCGAAGGGGTTTCTGGGAAACACTTGGGTGGCTCCGCCCCCTCACACAAGGGCCTCAGGTTTTACCCGGTAAGTCCCTAAGTGCCTCAACTGCCCTCTCATGTCAGCTGCCTCCTTGTCCCTCGATTTCGTTAGGGGACACTGTGCTATTCGTTCTTGATTTTCAAAGAGTTTTTAGGATGGAGTACCAGCAAAACCAGGTGGAAATAAAGTTGTCTGAACCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004892:ENSMUST00000090971:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.903
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=89.1)
A:
NA
C2:
NO
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:
CAGGAGAATGGGCTTTGGGAG
R:
GCAGTTGAGGCACTTAGGGAC
Band lengths:
357-661
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