MmuINT0005466 @ mm9
Intron Retention
Gene
ENSMUSG00000054672 | 5830411N06Rik
Description
RIKEN cDNA 5830411N06 gene [Source:MGI Symbol;Acc:MGI:2443685]
Coordinates
chr7:147481739-147482502:+
Coord C1 exon
chr7:147481739-147482044
Coord A exon
chr7:147482045-147482184
Coord C2 exon
chr7:147482185-147482502
Length
140 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TCAGAGTTTCTCCCTGTCAGGTC
3' ss Score
6.9
Exon sequences
Seq C1 exon
AGTTCCGACTGGTCAATGGCAGCAGCCGCTGTGAGGGCCGCGTGGAGCTTTTGGTACAGGATGCCTGGCAACCCCTCTGTGCTGCCAACTGGGACTTAGCAGATGCCACTGTGCTCTGCCACCAGCTCAACTGTGGCTATGCAGTGGCCACACCGCAAGGAGGCCACTTTGGAAATGTGGAAGGTCCCATCAGGACAGATGTGTTTCACTGTGTGGGAACAGAGCCCCACTTACTGAGCTGCCCAACAAGCACCTTAGGGGCCCAGGCATGCGCACTGGGGAATTCAGCCTCGGCTCTCTGCTCAG
Seq A exon
GTGAGTGCAGGCAGCCTTGAGACTGCGAAGAAGAAGGTAAACAGGACGAAGGTAAACAGTATGAGAGATTTGGGAGGGTGAGGATAGGTGGAGATGTTCGGAGCGATGGTCCTCTGCCCATCAGAGTTTCTCCCTGTCAG
Seq C2 exon
GTCTCCAGGATGCCCTTCGGCTGAGGGAGGGACAGAGTCACTGTGATGGCCGAGTGGAGGTCTTCCTGGATGGCACGTGGGGTCGTGTGCTGGACAGTGCATGGGACCTGCGTGATGCTGCTGTGGTGTGCAGGCAGCTTGGGTGCGGAGAGGCACAGCTAGCCTATGATGCGCCAGCACCAGGCCATAAGACCATTCCTGTGGGGCTGAGTCTGGTGCACTGCTTGGGCTCTGAGACCCACCTGACCCAGTGCAATGTATCTGCTTCTCTGCTGGTTCATGCAGGGACTTTGCGGGATGCAGGAGTGGTGTGCTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054672-5830411N06Rik:NM_001128145:5
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:
PF0053013=SRCR=WD(100=89.9)
A:
NA
C2:
PF0053013=SRCR=WD(100=91.6)
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:
ACTTAGCAGATGCCACTGTGC
R:
GTGACTCTGTCCCTCCCTCAG
Band lengths:
254-394
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: