MmuINT1030416 @ mm10
Intron Retention
Gene
ENSMUSG00000028495 | Rps6
Description
ribosomal protein S6 [Source:MGI Symbol;Acc:MGI:98159]
Coordinates
chr4:86856728-86857412:-
Coord C1 exon
chr4:86857321-86857412
Coord A exon
chr4:86856860-86857320
Coord C2 exon
chr4:86856728-86856859
Length
461 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
GTCCCCCTTTAAAACTGTAGCTG
3' ss Score
5.87
Exon sequences
Seq C1 exon
GAGAACTTAGAGCGCTATGTGCCCTGGGTTAAGCGGAAGTCGGGCCTCTTTTTCGTGACGCCTCCCAGGCGCTCGGCTGTGTCAAGATGAAG
Seq A exon
GTAGGCGTCCCCGGCCAGGGCCGAGTGAGGCCGCCCGAGCCCGAGCGTGCGGCACGGCCTCGGTCCCAGGCTCGCATAAGTCCCGCACTAAGTGGAGAAGGATCCGAGGCGGGAGGGAACTCGTTTTGGCGGCCCTGGGACGCTCTGGGAGAGCGGATGGCGGGCGATTGCAGCGCCGCCGCGGTGGACGTAGCGCCATAGCGGCGCCCGGCTCCGGGCCCGGCACGCGCGGTCCCGAAGCCCCGCTCGCGGCTGGCAGCCTTGCGGCTCTCGAGCCCTCGCCACTCTGCTAGCGGAGGTCTTGAGGGTCGCCCGGCGTCCTCAGCATCCCACAGAGCTCCTGTAAAATGTCCCGTGGATGCGGCGCTTTGCCGGGCGTGGGATCCGAGCCTCGGACGCCCTGCGTTGTCGGCCCGGCTTGGGTCCCTAAGGTTCTCTCTTGTCCCCCTTTAAAACTGTAG
Seq C2 exon
CTGAACATCTCCTTCCCCGCCACCGGCTGTCAGAAGCTCATCGAGGTGGATGACGAGCGCAAGCTCCGCACCTTCTATGAGAAGCGCATGGCCACGGAAGTAGCCGCTGATGCTCTTGGTGAAGAGTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028495:ENSMUST00000102814:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0109214=Ribosomal_S6e=PU(0.8=50.0)
A:
NA
C2:
PF0109214=Ribosomal_S6e=FE(33.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACTTAGAGCGCTATGTGCCC
R:
TCTTCACCAAGAGCATCAGC
Band lengths:
214-675
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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