MmuINT0005466 @ mm10
Intron Retention
Gene
ENSMUSG00000054672 | 5830411N06Rik
Description
RIKEN cDNA 5830411N06 gene [Source:MGI Symbol;Acc:MGI:2443685]
Coordinates
chr7:140295840-140296603:+
Coord C1 exon
chr7:140295840-140296145
Coord A exon
chr7:140296146-140296285
Coord C2 exon
chr7:140296286-140296603
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:ENSMUST00000164583:8
Average complexity
IR
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=95.1)
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
- 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