MmuINT0134923 @ mm9
Intron Retention
Gene
ENSMUSG00000036202 | Rif1
Description
Rap1 interacting factor 1 homolog (yeast) [Source:MGI Symbol;Acc:MGI:1098622]
Coordinates
chr2:51931601-51932628:+
Coord C1 exon
chr2:51931601-51931697
Coord A exon
chr2:51931698-51932500
Coord C2 exon
chr2:51932501-51932628
Length
803 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TTAAAATGCTTGTTTTTCAGAGG
3' ss Score
7.76
Exon sequences
Seq C1 exon
GCTCACATTTCCAGTCAGAACTCAGAACTGAGCAGTGCTGCTTTGCAAGCCTTGGGATTTTGTTTATATAATCCCAGAATTACCTCAGGATTGTCAG
Seq A exon
GTAGGGAAACTGATTAATATCTGTTGACTTTATAGTTTAAAACAGTTAAAGTACTGTTATCTATGGATAAATTGTTGCCTTCCCTCCTTAAGGTATTAATTTGGGACATGTGTGACTACATTGAACGCAAGAGTCATATCTACCATGTGGGTTCTGGGGACTGGACTTACTAGGCTAGATGTCAAGGGCCTTTACTGGCTCAGTCTTTTTAGTAGAACACAGTAAATTGGAAGTTAATATCTCTCTGTCTGTCTGTCTGATTTATGATTGATGTGGCAGTCATACCCCCTAAGGAACTCATTGTTGAGATGAAGAGTTCTTATATGATATTAATAAGTGTTATTTTGGAAGTGGTAGTAAAGTATAGTAGTGCTACTAAGTACTGTTAACTAGTACTATTGTTCTGTAGTTTGCAATTGTAAAAGAAACCTACAAGATCACTATTAGAGGAACTGAGGGGTAGGTAGTAAGGGGATATCATAAAGTTGTTACTCTTTCCTTCCCTCAGTAGAGTTGCAGTTTTTTCTTTTTTGTATAAAAGTCTCCATAATATCCTAAGATGACAATAGTTAATTGAGTATGATTAAAAAAAGGGTTTGCAGTTTGCAACTGTTTCCCCTTCGGTCAGGATTGTTTACTTTTTGCAAGAAGTGATATTGATCAGCATCTCTGTAGGTTTTGTGATCATCTGCACGTTCTGAACAGCTCCATCTACCTTTGTTACTTTTATTTTACTTTTGTAGTTGACATTTTAAAGATTTTAACTATACTACATAAATGAAATTAAAATGCTTGTTTTTCAG
Seq C2 exon
AGGCAAATATTCAAGAACTGCTTTTAACCTTGAATGGTATCATTAAGAGTTCAGACAAAAATGTGTGTACCAGGGCACTGTGGGTAATATCCAAACAGACGTTTCCTGCTGAACTTGTTAGCAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036202-Rif1:NM_175238:4
Average complexity
IR-S
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(8.8=100)
A:
NA
C2:
PF122313=Rif1_N=FE(11.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCACATTTCCAGTCAGAACTCA
R:
TTTGCTAACAAGTTCAGCAGGA
Band lengths:
222-1025
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: