MmuINT0005463 @ mm10
Intron Retention
Gene
ENSMUSG00000054672 | 5830411N06Rik
Description
RIKEN cDNA 5830411N06 gene [Source:MGI Symbol;Acc:MGI:2443685]
Coordinates
chr7:140297790-140298383:+
Coord C1 exon
chr7:140297790-140298104
Coord A exon
chr7:140298105-140298359
Coord C2 exon
chr7:140298360-140298383
Length
255 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
AACCTGCATTTCTTTTGCAGGTA
3' ss Score
10.72
Exon sequences
Seq C1 exon
AGGAAGGTGCACTTCGTGTACTTGGGGGTGAGAACGGCTGCTCTGGACGAGTGGAGCTCTGGCATGGAGGTTCATGGGGCACAGTGTGTGACGATTCCTGGGATCTGGCCGATGCAGAAGTTGTTTGCCGGCAGCTGGGCTGTGGCCCAGCCATAGCTGCCTTGCAGAATGCTGCCTTTGGCCCTGGTTCAGGGCCTGTATGGCTGGATGAAGTGGGATGCCGAGGCAGTGAGCTGTCTCTGGGAGCCTGCCAGGCAGAACCATGGGGATATGGAGACTGCTCCCACAAGGAGGATGCTGGTGTGCGCTGCCTAG
Seq A exon
GTGAGTGAGGCAGCCAGCAGTGGTGAGAAGAGGGATGCCAGGTTGATATTTTCGGCCGTTTTCACCTTTGTTCTGCTCAGACAAATTCTTGAGCACAGGACTCCAGTGTTCAGGGTTCCACTGGTGTTCCAGGGATGGCTGCCACCCTCAGTTCTGCATAGCTCCTGCTGACCTATTGGCTACCACCCGCAAAGGTTGGGCCCATCTATGCTGTTGAAGGTGATGATACTTCCCCAACCTGCATTTCTTTTGCAG
Seq C2 exon
GTATCCCTGGAACCATGGCATCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054672:ENSMUST00000164583:13
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=0.111
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=92.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTGGACGAGTGGAGCTCTG
R:
ATGCCATGGTTCCAGGGATAC
Band lengths:
296-551
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