MmuINT0133955 @ mm9
Intron Retention
Gene
ENSMUSG00000039316 | Rftn1
Description
raftlin lipid raft linker 1 [Source:MGI Symbol;Acc:MGI:1923688]
Coordinates
chr17:50141957-50143682:-
Coord C1 exon
chr17:50143579-50143682
Coord A exon
chr17:50142039-50143578
Coord C2 exon
chr17:50141957-50142038
Length
1540 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
CCTCGGCTCCTGTGTTATAGGGA
3' ss Score
8.85
Exon sequences
Seq C1 exon
GGTACAGAGGTACAGACCGACTACATGCCCCTGCTGAACTCGCTGGCGGCCTACGGATGGCAGCTCACCTGTGTGCTGCCAACGCCTATACTCAAGACTACCAG
Seq A exon
GTAACAAACATAGCGACCTTTATGACATTCATGGGTGAAACGTGAAGCTCAGGCCTGAGGCCCAGTTGGCAGGAGGTAGCCAAAACAGGGCCTAAGACCTCAGTATACAGAGTTGGGCTCCTGCCCTGCACCTGGCTGCCTCTCTGCTGACCTATAGTGATAGCCCTCTCTCCTCTCCCTACCCCATGGCCCTGAAGATTTCTGCCTTTAATGAATTCACTGCAGTTTCACACTACAGGCAACAGCAGGTGTCCTGGGCTGGTTGACAGTGGGATAAAAGCCATGCTAGCCCGTGGCCTTCCTAGACCCCTCTTCCGGCTCCTCTGGGTCTTCTCATTCCGCAGTGTGCTCCCCTGCCTGTTCTTGGCAACATTTGGCCACTGGGAACCACTGGGCTCCTTTTCAAGACCAAGTCTTGTCCAGGCAGAGGCTGATAGTGGAGCAGAAAACACCCAGAAGCCTGCCATTTGCTACCTATGTCACCCTGGCTAAGTCCCACACCCTATCTGAGTGTTCCCTAGTTATTTCCAGAGGACACAACCATGATGGAAATGAGTTTTGGCCAGGAAGACCCAGTGCTCTGAGGGATGTGAACCCCAGGGGTACACAGAGCTGTCTCAGAGACGCACACTTATTCCCTCATCTTCACGCTGGTGAATGGACAGCCTGGGAATGTGCTGGTCTATCCGAATCCTCCCAGTGTGAACTCTGGGCTGAGTGTTCCCTTCTGGTTTGTCAGAGAAGTTGCAGGCTGCTAGCGGTAGGGTGGAGACCCAGCCTCTGGCAAAGCTGCAGTGCTAGCTAAGGCACTAGATCTCCCTTCCTTGATCTCTGGGCTGAAGGCAGTCAGAGGCGGTTACAAAAGAGTTAAGGTGAACAGAAGGGTGGAGGTGGAGAGAACCGGCAGTCACCTTTAGTATTTCTATCCAAGGCACAGCATGGGGTCCTGCCTTTTTCTGACACACAGCTCTCAAGCTCTCTATTTCTCTTTCCATAGGTGTGAGTCAGAGTTAATTACCATGTCCATCTTGCAGCTAGCGCCTGATATCAGTGTGTCTGTAGGGGTGACACAGTAGCCTACATATTTATCAGCTCTCCCTATACCACCTTCATGTCACACTGGAGGGCTAAACTCATGGCCTGTCTTTATTCTCCTATGCAGCCTACCATGACTACCAAAGACAGAATTGGAAGGCAACTCTGTTCTTTTGGGGACTCCCTAATCTGCCACTATATCCTCACTTAACCAAGGCACCAGCTGCCACTGCCTATCAAGAGCATGGGAATTTTTAGCCAGGAAGTAGAGATAGCCAGGCAGAATTGGTTGGTATCTAAGATAACCCTTGACTTAAGAGTGGGAACTCTGACTTCCAGTCTTAAGTCAGGCAGCAGCCTTCCTTTACTTATAGGAAGTTCAGGATTACACCCATGGGGAGAGGATGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTTGTGGGGTGGGGGGGTGGGGGGAGATGTTAATCCTCGGCTCCTGTGTTATAG
Seq C2 exon
GGAAGGGAACGTGTCCACCAAGCAGATTGTGTTTCTTCAGAGACCATGTCTACCTCAGAAAACCAAGAAGAGGGAATCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039316-Rftn1:NM_181397:8
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:
PF152501=Raftlin=FE(16.4=100),PF137831=DUF4177=FE(57.6=100)
A:
NA
C2:
PF152501=Raftlin=FE(13.0=100),PF137831=DUF4177=PD(25.4=53.6),PF051329=RNA_pol_Rpc4=PU(28.9=78.6)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: