MmuINT0165257 @ mm9
Intron Retention
Gene
ENSMUSG00000020773 | Trim47
Description
tripartite motif-containing 47 [Source:MGI Symbol;Acc:MGI:1917374]
Coordinates
chr11:115969580-115971330:-
Coord C1 exon
chr11:115970848-115971330
Coord A exon
chr11:115969676-115970847
Coord C2 exon
chr11:115969580-115969675
Length
1172 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGG
5' ss Score
4.41
3' ss Seq
TCACAAAACCTGGTCCACAGGTG
3' ss Score
6.53
Exon sequences
Seq C1 exon
AAGAACCACACGCTGTCCGAGTTGCTGCAGCTCCGCCAGGGCTCGGTCCCGGGACCCATGTCCGCCCCGGCTTCAGGATCGACCCGGGGCGCCACGCCCGAGCCCTCCGCGCCCAGCGCACCACCTCCGGCTCCGGAACCATCGGCTCCCTGCGCGCCGGAGCAGTGGCCCGCGGGTGAGGAGCCGGTGCGCTGCGACGCGTGCCCCGAGGGCGCCGCCCTGCCCGCCGCGCTCTCTTGCCTCTCCTGCCTCGCCTCCTTCTGCTCCGCGCATCTGGCCCCCCACGAACGCAGCCCCGCCCTGCGCGGCCACCGCCTGGTGCCCCCGCTGCGCCGACTTGAGGAGAGCCTGTGTCCGCGCCACCTGCGGCCTCTGGAGCGCTACTGTCGCGTGGAGCGTGTGTGCCTTTGCGAGGCCTGTGCCACTCAGGACCATCGCGGCCACGAGCTCGTGCCGCTGGAGCAGGAGCGCGCGCTTCAGGAG
Seq A exon
GTGGGGCACCTTGAGTCGACACGTGGAGATGGGTGACAGGAGGGACACTAGAGCTATTTAGTCCCTCACTCTTATCCGGGTGTGTCTGTTATATATTTGTTTTATCATTATGGCTGTGCACATGGAGATGAAGGAAGCAACTTTGTGGGGTTGGTTCTCTCCTCCTGCCTTTACATGGGCTTCATCTCTCTGACTCAATAGGCTCTGCCTTAGTTTCCTCCTCTAGCCTGAGAATCTTTGCAACCTCTTCCGGTCTACACTGTCATTTGCTGGGGCTGGTGTGGATGGAAAGAGAGTCGGGAGGGACTAGTAAGATGAAAGAGTGGCAAAAAGCCGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGCTTTAGCTAGATTAGTGTAAGTGTAAAGCGAGAGAGGGATCCGCATTAGGCCCTCAGAAGCCGTGGGGGTCAGGAGTCGCTGGGTGCGGGCGGGGCCCCGTAGCTGATGCCCTCTTCAATTCAGATTCGTCCTGAATTGAGTCAGCCACTTTGTATGGGTGTGGCGGGCACCAGGAGAGCGACGGAGTTTGGGCTGGTCACACAGATCTCCTCTGTCCGAATGCTCTGGGGCCGTGGGGAGCATGTGCCCAGTGTCCCGCTACCTCCCACCCCCAGTTTCCTTTGGCCTCCATCCCGGTCTTGGCGCCTCTGGCTTTGGGATTTTCCGCCTCTCCTGCCTGGAGCTGTGACTCATTAGAGCCGAGGGATTTGCCCGGAATCCCCATTTTTCAGAGCTGGATTGGGGGTGAAGGCTCTTTTGAGACTAATCCCCAGGACTATTTAGTGTCCTCTTTTCTGGTTCCGTCACGTCACACCCTACCCCACCCTCTCACACTTTGCCTCTTCCCCAGGGGGAAAACAATCCCAAATAGAGAATCATAGGTGGCCCTATACTGGCTTCTCTGGTCAACAGGTTGTCATATGCCCACAACCTGCTTCCTTGCCAGGCATTTGGAAATGGCACCAGCTTGGGCCAGAGCTGCCTTGGGGATATTCTGGGACTTCACGGCCATTTCCGTTCCCTTCATTCACAAATGTCACTACCTAGCCCCCCAAATTCTGAGATCTGATGCAGTTCCGGGGACCTTTGACAGACACCAATCTCACAAAACCTGGTCCACAG
Seq C2 exon
GTGGAGCAGTCCAAAGTCCTGAGCGCTGCGGAGGACCGCATGGATGAACTGGGTGCCGGCATCGCACAGTCCCGCCGTACTGTGGCCCTCATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020773-Trim47:NM_172570:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.323 A=NA C2=0.219
Domain overlap (PFAM):
C1:
PF152271=zf-C3HC4_4=WD(100=21.8),PF0064319=zf-B_box=WD(100=17.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCTTGCCTCTCCTGCCTC
R:
CTTGATGAGGGCCACAGTACG
Band lengths:
348-1520
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: