MmuINT0164885 @ mm9
Intron Retention
Gene
ENSMUSG00000064043 | Trerf1
Description
transcriptional regulating factor 1 [Source:MGI Symbol;Acc:MGI:2442086]
Coordinates
chr17:47463672-47464053:+
Coord C1 exon
chr17:47463672-47463811
Coord A exon
chr17:47463812-47463949
Coord C2 exon
chr17:47463950-47464053
Length
138 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
TGACTTCTTATTCTCAACAGTGG
3' ss Score
7.58
Exon sequences
Seq C1 exon
ACGCATCAACATTGGCTTAAGGTTCCAAGCAGAGATCCCAGAACTGCAAGACGTCTCCGCCCTGGCTCAGGACACACACAGGGCCACACTGGTATGGAAGCCGTGGCCTGAGCTGGAAAACCAGGCCCTCCAGCAGCAAG
Seq A exon
GTACTGGCACTTAGGAGGAGCTGGGGATAAAGCTGGCTTCTCTTAGATGTTCTCTAACAGGAACATCTGGCCCCAGAATGGGTGTGGGATTTTGTGACACTGAACATTTCTGATACAATGACTTCTTATTCTCAACAG
Seq C2 exon
TGGAGAATCTTCTGAATTTGTGTTGTTCCAGTGCGCTGCCAGGTGGAGGAACCAATTCGGAATTTGCTTTGCACTCTCTCTTTGAGGCCAAAGGTGACGTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064043-Trerf1:NM_172622:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0144819=ELM2=PU(78.9=93.8)
A:
NA
C2:
PF0144819=ELM2=PD(19.3=31.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCATCAACATTGGCTTAAGGT
R:
CATCACGTCACCTTTGGCCTC
Band lengths:
243-381
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: