MmuINT0024318 @ mm9
Intron Retention
Gene
ENSMUSG00000004892 | Bcan
Description
brevican [Source:MGI Symbol;Acc:MGI:1096385]
Coordinates
chr3:87793090-87794220:-
Coord C1 exon
chr3:87794062-87794220
Coord A exon
chr3:87793173-87794061
Coord C2 exon
chr3:87793090-87793172
Length
889 bp
Sequences
Splice sites
5' ss Seq
ACGGTGGGT
5' ss Score
8.27
3' ss Seq
CCTCTGGCTTTTCTCTCTAGATC
3' ss Score
10.8
Exon sequences
Seq C1 exon
GCCTTCATTTCTGCAGCCCTGGCTGGGAGGCCTTCCAGGGAGCCTGCTACAAGCACTTTTCCACACGAAGGAGTTGGGAGGAGGCAGAAAGTCAGTGCCGAGCGCTAGGTGCTCATCTGACCAGCATCTGCACCCCTGAGGAGCAAGACTTTGTCAACG
Seq A exon
GTGGGTGGGGCCTGACTTCCTGCGCATGCTCCAGGCCAAACCCACTCCTCACCCACAGCTTCCTCACTCACGCCTCTTCACTCCTCCCTCTCTCTCCCTCTTTCCTCTCTCACACCCCTTTCCCCTTCCCTCATCTTTTACCTCTCACTCACCCGGAGACCTGTTGTGGGGAGATTGGGCCCATGGTGTCCGACATTTGCGGGGCTGCCTAGGCTGCGGGGGTGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTCCCTGCTTTCCCGGATGCAACTGTTTCCCTAACTCTGTGGTAGCAAGGTTTGCTCCTCTTCTTTCCCTTCCAAAGTGCTATTCTCCACCTGCATGTCCTTGCGCCATGGATGTGAAGGTTACTTACGAAAATAGGGAGACAGGCTAGAGAGATGGCTCCGCGGTTAAGAGCACTGGCTGCTCTTTTGAAGGGCCCAGGGTTCAATTTCCAGCACCCACATGACAGCTCACAACCATCTGTAATTCCCGTTCCGGGTTGCCCCTCTGATGCCTTCTGGCCTCTGAGGACGATGCACACAAGTGGTGCACAGACACAAATGTATGTGAAATACATACAACAAAAATTCAAAGCTTTCAAAAGAAGAGAATTTAGGGAGAGCCTTTATGATAGCAAATCTGATTGTCTTCCCTGGGGGGGGGGGGGGGAGAAAGACAGAAAAGGTGGGTGAACGCCGTCCATCTTTGGCTGCTTTCCCAGCAGAAGAGGCTAGGTCTGAGCCAACAGCCACAAACCAGCAAGATTTGGGGAGGTTTTTGGATGGACTCCCCAACAGGTCATCACTGGCCCAGAAATACTGGGCTTCCTGCTCACTGCACCTCTGGCTTTTCTCTCTAG
Seq C2 exon
ATCGATACCGGGAGTACCAGTGGATTGGGCTCAATGACAGGACCATCGAGGGTGACTTCTTGTGGTCAGATGGTGCCCCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004892-Bcan:NM_007529:10
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:
PF0005916=Lectin_C=PU(30.2=59.3)
A:
NA
C2:
PF0005916=Lectin_C=FE(25.5=100)
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:
CCTTCATTTCTGCAGCCCTGG
R:
GAGGGGCACCATCTGACCA
Band lengths:
239-1128
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: