MmuINT0018938 @ mm9
Intron Retention
Gene
ENSMUSG00000038352 | Arl5c
Description
ADP-ribosylation factor-like 5C [Source:MGI Symbol;Acc:MGI:3028577]
Coordinates
chr11:97856381-97857487:-
Coord C1 exon
chr11:97857132-97857487
Coord A exon
chr11:97856442-97857131
Coord C2 exon
chr11:97856381-97856441
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
CTCGCAACACTAAAGCAGATAGTTCCAACTTCAGTTTTCTCAGGGTAAAGAGGACTCTGGGATTTTCCTTGCACTTTCCTGCCCCTAGACAAATACCTAGTCTTCGTGGTGACGCCACTCAGACCCTCAGCACCGAGAAAGAGCCAGCGTCCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCAGCGGGTCTGGCCCTCCCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGGAGGCTGCTGAGCCCCGCCCGCCCCCAGCTCCGGGAGTGCCATGGGACAGCTGATAGCCAAGCTGATGCGAATCTTTGGGAGTCAGG
Seq A exon
GTAAGCGGCGCACCGGGCAGCCCAGTGACCTCTTTGATTCCGCTGTCTTCTGGGGCTCTTGGGATTTTGGAGTCGTCCGTGAAGACTGACTGGGAACCTTGCGCTGCTAGAGTTGGATTTGTGCACTCCCATACTCTCCATGGCCTCCTGCCTGCTCTCCTCCCACAAGCCCCCCGCCCCCCACCTTGACCCCGCGCTTCAGTGTGCCCAGTGCACAGGGGTGGGAGAGCCTTCTGCCTCTGACCCCACCACCCAGCTGAGCTGTGTGCGACCCTGAGGGCCCCCAAAGTCAATTTCCTGAGATTGTGATTTAGAGCCCAGTGTGCTTCGGACCCTTTAGACGATCGCTGTCTAGAAATGTAGACGGAGGTGGGGTAGGGGGTCAGGAGGGGTGCAGGGGTCCGGTCCGATGGCAAGTGAAACGGTACAGTCTTCGACAGAGGTCCCCCGGACCGCGTTTCTCTGAGCATCCTAGGAAATTGGGGGGGGGGGCGCACACAGAAAGCTGAGATACCGAGCTTTAGCTCGGAGATTGCCAAGGGATGTGTGGAGCCGGGAGAGAAGGCATCCATTCATCCAGACAAGAGCAGAGGGTGAGGAAGAGGCCAGGACGAGAAGCCTACTAGGGACACCCACGCCCGCAGTCGTCCGGGTTGGCTCTGACCTTGCCCTTCCCCTGGATGCCTCCAG
Seq C2 exon
AGCACAAAGTCATTATCGTGGGACTGGACAATGCAGGGAAGACCACCATTCTCTACCAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038352-Arl5c:NM_207231:1
Average complexity
IR-S
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:
PF128032=G-7-MTase=PU(23.0=87.5),PF0002516=Arf=PU(8.5=93.8),PF0282614=2-Hacid_dh_C=PU(5.2=43.8)
A:
NA
C2:
PF128032=G-7-MTase=FE(32.8=100),PF0002516=Arf=FE(11.4=100),PF0282614=2-Hacid_dh_C=FE(14.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: