MmuINT0133912 @ mm10
Intron Retention
Gene
ENSMUSG00000020696 | Rffl
Description
ring finger and FYVE like domain containing protein [Source:MGI Symbol;Acc:MGI:1914588]
Coordinates
chr11:82811028-82812810:-
Coord C1 exon
chr11:82812400-82812810
Coord A exon
chr11:82811112-82812399
Coord C2 exon
chr11:82811028-82811111
Length
1288 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
GCACCTTTCTCTTCCCACAGGCC
3' ss Score
12.29
Exon sequences
Seq C1 exon
CAGACCTGCTTGGACTGTAAGAAAAACTTCTGCATGACTTGTTCGAGCCAAGAGGGGAATGGGCCACGCCTCTGCCTTCTCTGCCTACGGTTCCGAGCCACGGCCTTCCAGCGGGAGGAGCTCATGAAGATGAAGGTGAAGGACCTGAGGGACTATCTCAGCCTCCACGACATCTCTACGGAAATGTGCCGGGAGAAAGAGGAGCTGGTGTTCCTGGTGCTTGGCCAGCAGCCTGTAATTTCTGAGGCGGACAGGACTCGTGTTCCCCACTTGCCCCAGGCCTTCCCTGAGCAGCAGGCCTTCCTGACCCAGCCTCAAACCAGCACAGTGCCTCCTACCTCACCTGGCCTCCCTTCTTCACCTGCACAAGTCACCTCTGTCCCCTTAGCCCAGGATCAGGAAACTCAGCAG
Seq A exon
GTAGGAACCACCACGCAGCCTCTTCACCGCTGTGTCTGCTCTGGGACTCTTTTTATTCCCTCCGCTGCATTGTGGGAGTGGGGTGTCAGGTGTCATGTCTAGATGGTGTAAAACCTTTCTGCTTGTTGATTCTAGAAGTGGTGTTTTCTGATCATTAGGCTCAAGCTCTGACTTCAGGGAAGGTAGGCCTAGTAGTACTGTGTTTTTGTGCAGTTTGTTTGTGATACCTTCATCCCCTAATTAGACTTAAAAAAATCTTCTTTTCATTGCTTCAGAAATACTTTGAGGAAAATCATTCTCATCTCTAGTTTGCCCTTCAGTTTGCTGCCCTTTTGACTGATCTAAGTGGCAGGAGAGGAGAGCAATGGGGAGCATTGGGGAGGGCGGGCCTTGCCGCTGTCCTGCATACCATGTGCGAACAGAACAGCGGTGGCCAGCATGCTGTGGGGCTGTACCCTGCCTCCCTGTTACATAGTGTTGCCTGGAAACGGTAAGCCAGGAGCAGCCAGTTGGGTTGTGGGGAGTCCACAGTCAACACGTACCGTCTCCACCCTCGGGAAGCCCTGACAGAGAAAGGCTAAGCACGAGACCCGCTCTGAGGTTTGTCTGGGGTTTGTCAGGAGTGGTGGTGTCACAAAGATCTGCAGAAGTCTCTCACTCATTCTGCAAGTCACAGGGCTTGGGCACAGAAAGATTAGGACCTAGATCTCTATCCACTGTCATCGTCCCCCCTCCCTCCCCCCTTTGCACTGTCCTGAAACTCACTCTGTAGATCACACCAGGCTGACCTCAAACTCAGAGATCCACCTGCCTCTGCCTCCTGGGGCAGAGTGCTGGGCTTAAAGGCGTGTCCCCACCACGGGCATGAATGAGGTGTTTGAACAAACTAGTGGACACTGGTGCAGAGGCAGAACCGTGGGAGTGGGTGGAGGCTGTGGGGAGGGCATTGGGTTAAGACAGTCTGCTGGAGAGACACCTTTCACCTCAACTGTCCAGGCTGAGCACAGACTGGTGATGCGTGGCGGCTAATGCCACCCTCACTGCTGGGCAAAATTAGCACACTCTTGTACTTGATGCAGCTTTCCATCTGGTGAACTCTGTGTGTATCATCTCTGGCTGTGAGATTCGGCTGTTAGACAGCAGGCATTCGTGGTCCTCCTTCGGGAGCCTTGTTTCTGGAGGGAGACGGGAATACACTTTTGGACATTCGTGTGAACTGAGAGCGGCCCATGGTTTGTAAGTCACTGGGCATCTCTGTGGCTGTGATGGCACCTTTCTCTTCCCACAG
Seq C2 exon
GCCGTTGGCCATGTGTCTCAGGACCACGAGGAGCCCATCTTCCCGGAGAGCACAGCCAGAGTACCTACTGAGGATGAGACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020696:ENSMUST00000074515:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.359 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0231811=FYVE_2=PD(67.2=32.8),PF102084=Armet=WD(100=48.2)
A:
NA
C2:
PF102084=Armet=PU(26.5=96.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAAGGACCTGAGGGACTA
R:
AGGTACTCTGGCTGTGCTCTC
Band lengths:
343-1631
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