MmuINT0018938 @ mm10
Intron Retention
Gene
ENSMUSG00000038352 | Arl5c
Description
ADP-ribosylation factor-like 5C [Source:MGI Symbol;Acc:MGI:3028577]
Coordinates
chr11:97995067-97996181:-
Coord C1 exon
chr11:97995818-97996181
Coord A exon
chr11:97995128-97995817
Coord C2 exon
chr11:97995067-97995127
Length
690 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGC
5' ss Score
9.04
3' ss Seq
CTTCCCCTGGATGCCTCCAGAGC
3' ss Score
6.28
Exon sequences
Seq C1 exon
TCACTCTACTCGCAACACTAAAGCAGATAGTTCCAACTTCAGTTTTCTCAGGGTAAAGAGGACTCTGGGATTTTCCTTGCACTTTCCTGCCCCTAGACAAATACCTAGTCTTCGTGGTGACGCCACTCAGACCCTCAGCACCGAGAAAGAGCCAGCGTCCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCAGCGGGTCTGGCCCTCCCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGGAGGCTGCTGAGCCCCGCCCGCCCCCAGCTCCGGGAGTGCCATGGGACAGCTGATAGCCAAGCTGATGCGAATCTTTGGGAGTCAGG
Seq A exon
GTAAGCGGCGCACCGGGCAGCCCAGTGACCTCTTTGATTCCGCTGTCTTCTGGGGCTCTTGGGATTTTGGAGTCGTCCGTGAAGACTGACTGGGAACCTTGCGCTGCTAGAGTTGGATTTGTGCACTCCCATACTCTCCATGGCCTCCTGCCTGCTCTCCTCCCACAAGCCCCCCGCCCCCCACCTTGACCCCGCGCTTCAGTGTGCCCAGTGCACAGGGGTGGGAGAGCCTTCTGCCTCTGACCCCACCACCCAGCTGAGCTGTGTGCGACCCTGAGGGCCCCCAAAGTCAATTTCCTGAGATTGTGATTTAGAGCCCAGTGTGCTTCGGACCCTTTAGACGATCGCTGTCTAGAAATGTAGACGGAGGTGGGGTAGGGGGTCAGGAGGGGTGCAGGGGTCCGGTCCGATGGCAAGTGAAACGGTACAGTCTTCGACAGAGGTCCCCCGGACCGCGTTTCTCTGAGCATCCTAGGAAATTGGGGGGGGGGGCGCACACAGAAAGCTGAGATACCGAGCTTTAGCTCGGAGATTGCCAAGGGATGTGTGGAGCCGGGAGAGAAGGCATCCATTCATCCAGACAAGAGCAGAGGGTGAGGAAGAGGCCAGGACGAGAAGCCTACTAGGGACACCCACGCCCGCAGTCGTCCGGGTTGGCTCTGACCTTGCCCTTCCCCTGGATGCCTCCAG
Seq C2 exon
AGCACAAAGTCATTATCGTGGGACTGGACAATGCAGGGAAGACCACCATTCTCTACCAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038352:ENSMUST00000042971:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002516=Arf=PU(17.4=93.8)
A:
NA
C2:
PF0002516=Arf=FE(11.4=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:
CTTGCACTTTCCTGCCCCTAG
R:
GAGAATGGTGGTCTTCCCTGC
Band lengths:
342-1032
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