MmuINT0004442 @ mm9
Intron Retention
Gene
ENSMUSG00000070883 | 4930578N16Rik
Description
RIKEN cDNA 4930578N16 gene [Source:MGI Symbol;Acc:MGI:1923100]
Coordinates
chr2:69619696-69620175:-
Coord C1 exon
chr2:69620002-69620175
Coord A exon
chr2:69619890-69620001
Coord C2 exon
chr2:69619696-69619889
Length
112 bp
Sequences
Splice sites
5' ss Seq
CACGTACGA
5' ss Score
5.74
3' ss Seq
ATAGTGTGATCTTTTTGTAGTCA
3' ss Score
4.44
Exon sequences
Seq C1 exon
GGAATGAAAGAACAGAAACTTAAAGCCAAGCAAAAGCGTGATGAAGAGATTGAGGCTGAAAGAAAAGTTCTTGATCTGGAGGAAGAAATATACAAAGAAGGAGAAAGAAAGAAGGCCATTGAGAGTGCTAGGCAGTGCCAGTTTCACCAGACGGAGCGAGTGAAGCGCTTTCAC
Seq A exon
GTACGATCTGCTTCTCTTCTACTTACATATGTGGATATTTAACATGCACAGTTAACAGTTTTCCCTATAGCATTATACATCGTTTTCTTAAAATAGTGTGATCTTTTTGTAG
Seq C2 exon
TCAGGACTTCTTCTCAGCAGAGTTATGAAAGAGCGTGATGTCCAGATTCAGTACAAAAAGAATGCAGTGAAATCAGATAAAAAATGGGAGGAGCAAGTGAAGCTCAACGATGAAAAAGCTTTTAAAGAAGACCAAGAGAAAGAAGAAAAACGGCGCAGAGAAAGAGTAGCTCTTGCCGAGGATCATCTGAAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000070883-4930578N16Rik:NM_001077684:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.293 A=NA C2=0.426
Domain overlap (PFAM):
C1:
PF138681=Trichoplein=PU(2.7=15.5)
A:
NA
C2:
PF138681=Trichoplein=FE(19.1=100)
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:
GCCATTGAGAGTGCTAGGCAG
R:
AGATGATCCTCGGCAAGAGCT
Band lengths:
248-360
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: