MmuINT0165259 @ mm9
Intron Retention
Gene
ENSMUSG00000020773 | Trim47
Description
tripartite motif-containing 47 [Source:MGI Symbol;Acc:MGI:1917374]
Coordinates
chr11:115968738-115969322:-
Coord C1 exon
chr11:115969092-115969322
Coord A exon
chr11:115968937-115969091
Coord C2 exon
chr11:115968738-115968936
Length
155 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGGGCATTTGTCTGGCACAGGAG
3' ss Score
5.15
Exon sequences
Seq C1 exon
AGTGCAGCTGTGGCAGAGCGGGAGAGGGTGAGCCAGATGTTTGCCGAGGCCACAGCCACCCTTCAGAGTTTCCAGAACGAGGTGATGGGGTTCATCGAAGAGGGAGAGGCCACAATGTTGGGCCGGTCCCAGGGTGACCTGCGTAGACAAGAGGAACAGCGCAGCCGCCTAAGCAAGGCACGGCACAACCTCGGTCAGGTTCCAGAGGCGGATTCAGTCAGCTTTCTCCAG
Seq A exon
GTGAGGGCGGCTCAGGAGCCATAATTGAAGAGATGGGGCGGGGTTGAGAAACAATGGCAGCCAGGATGGGTACCTGGCCTTCCAGGATAGTTGCTACCTTCCCTGGTGGCGAGACACTGTGGCCAGCAGACTTACTGGGCATTTGTCTGGCACAG
Seq C2 exon
GAGCTCCTGGCACTACGGCTGGCCCTGGAGGAGGGGTGCGGCCCCGGGCCTGGGCCCCCCAGGGAACTCAGCTTCACCAAGTCCTCCCAGGTGGTCAAAGCGGTGAGAGACACCCTCATCTCAGCCTGTGCCAGCCAGTGGGAGCAGCTGCGGGGGCTGGGCAGCAATGAGGATGGGCTACAGAAACTCGGCTCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020773-Trim47:NM_172570:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.338 A=NA C2=0.381
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGTTCATCGAAGAGGGAGA
R:
TTTGACCACCTGGGAGGACTT
Band lengths:
244-399
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: