MmuINT0134924 @ mm10
Intron Retention
Gene
ENSMUSG00000036202 | Rif1
Description
replication timing regulatory factor 1 [Source:MGI Symbol;Acc:MGI:1098622]
Coordinates
chr2:52076981-52077287:+
Coord C1 exon
chr2:52076981-52077108
Coord A exon
chr2:52077109-52077192
Coord C2 exon
chr2:52077193-52077287
Length
84 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TATGCGTTTTTGTCATTTAGGTA
3' ss Score
9.88
Exon sequences
Seq C1 exon
AGGCAAATATTCAAGAACTGCTTTTAACCTTGAATGGTATCATTAAGAGTTCAGACAAAAATGTGTGTACCAGGGCACTGTGGGTAATATCCAAACAGACGTTTCCTGCTGAACTTGTTAGCAAAATG
Seq A exon
GTGAGTCTAGTTTTGGGACATCTGAATTATATGCCCAAAAGACAGTTGTGGCTCACCTGATTGGTATGCGTTTTTGTCATTTAG
Seq C2 exon
GTATCCAGTATTATTGATTCATTGGAAGTGATACTAAGTAAAGGAGAGATACATTCTGCTGTTGTTGATTTTGAAGCATTAAATGTTATTATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036202:ENSMUST00000069794:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF122313=Rif1_N=FE(11.5=100)
A:
NA
C2:
PF122313=Rif1_N=FE(8.5=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:
AGAACTGCTTTTAACCTTGAATGGT
R:
ACAACAGCAGAATGTATCTCTCCT
Band lengths:
180-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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