MmuINT0005188 @ mm10
Intron Retention
Gene
ENSMUSG00000040412 | 5330417C22Rik
Description
RIKEN cDNA 5330417C22 gene [Source:MGI Symbol;Acc:MGI:1923930]
Coordinates
chr3:108480976-108481369:-
Coord C1 exon
chr3:108481264-108481369
Coord A exon
chr3:108481126-108481263
Coord C2 exon
chr3:108480976-108481125
Length
138 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
ATACCATTCTTTCTTCCTAGGGG
3' ss Score
10.37
Exon sequences
Seq C1 exon
GTTGAGCTAAATAGAGGCAATAACGTCCTCTATTGGAGAACCACAGCTTTCTCGGTGTGGTCCAAAGTGTCCAAGCCCGTGCTTGTTAGAAACATCGCCATAACAG
Seq A exon
GTACAGAAAACAGCTTGGATCTGGGTCTGCTGCTGGCTTCCTGGACTCCTGGCTTCTAGGGAGGGATGGGCATTTGGTCCCCAGGGCCTTGGTGTCTGGGCTCAAGCTTTGATCGTCTATACCATTCTTTCTTCCTAG
Seq C2 exon
GGGTGGCTTACACCTCCGAGTGTTTCCCCTGCAAGCCTGGCACATACGCTGCCAAGCAGGGCTCCCCTTTCTGCAAGCTTTGTCCAGCCAACTACTACTCAAACAAAGGAGAAACGTCCTGCCATCCGTGTGATGCTGACAAATACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040412:ENSMUST00000106625:6
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:
PF076998=GCC2_GCC3=PU(0.1=0.0)
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=64.7)
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:
AGAGGCAATAACGTCCTCTATTGG
R:
GAGTATTTGTCAGCATCACACGG
Band lengths:
242-380
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