MmuINT0018941 @ mm9
Intron Retention
Gene
ENSMUSG00000038352 | Arl5c
Description
ADP-ribosylation factor-like 5C [Source:MGI Symbol;Acc:MGI:3028577]
Coordinates
chr11:97853596-97854822:-
Coord C1 exon
chr11:97854739-97854822
Coord A exon
chr11:97853748-97854738
Coord C2 exon
chr11:97853596-97853747
Length
991 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
GATGGGTCTTCTGCCTACAGGCA
3' ss Score
8.38
Exon sequences
Seq C1 exon
TTTGTCATCCTTGTGATAGATAGCACAGACCGGAATCGGCTGCTCACCACCCGGGAGGAGCTGTATAAGATGCTGGCCCATGAG
Seq A exon
GTAAGCCTCCCCCTGTGCCCCCCCCCCCCCCAACTCGGGAAGCCATCCAGTGAGATTAGCCGTGTACTCTCAGACTGGTCACACACCCTCTCTGAAGTTCATTTCTTTTCTTTCTTTTGTTTTTGTTTTCTTCAAGACAGGGTTTCTCTGTGTAGCTCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTTGAACTCAGAAACCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAGGTTCATTTCTGAGATGCTAATTTGAAAGCCCTATCCTTGTAACATGGGGAGAGCTAGTTTACTACAGATAAAGGGTTCTGTCAGTGCCCCCAGAACCACTGCGCACAATTTCTGGTTCAAGGGCTAATCTCACCTCTCACCCATTGTGAGACCCCGAGAAAGTTGTTTCATTTCTAATAAGTTGCTCCACTTCTAATAAATCAGACCATTAGATCCCATCTCACAATGGGAGTGGTGGCTTTTGCCTACATTCTGGGCAACTGAAGCAGATTGTCATGAGGTTGAAGCCTGCCTGGGCTCCATATTGAGTTCCAGGCCAGCCTGGGTTACAGAATAAGATTTTGTTTTGAAAAAACAAAATGGACAGTGGTGGCACATGCCTTTAATCTCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTTGAGGCCAGCCTGGTCTAGAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACTCTGCTTCAGTGGGGAAAAAAAAAATCCTAAAAAACAAAATTACCAATGTCTGAGGTTTTGCAAGCATCCTGTGAGTGGTTGGAATGTGTTCCGAGAGCTGTGGCTTCATTAGATGGGCTGCTGATGTCAGGGTGGGCCTCCACCTCTGTCCCCCCTGGCATGGGCCTTTCTCTAGGACAGTGGGGCAGGGATCCTAGAGGACTGTGGGAGGGATGCTGCGCTGGCTGGCTGGCTGACATGGATGGGTCTTCTGCCTACAG
Seq C2 exon
GCACTTCAAAATGCTTCAGTACTGATCTTTGCCAACAAGCAGGATGTGAAAGACTCCATGACCACAGCAGAGATCTCCCAATTTCTCACACTCAGTGCCATCAAAGACCACCCGTGGCATATCCAGGGCTGCTGTGCTCTCACAGGAGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038352-Arl5c:NM_207231:4
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:
PF0002516=Arf=FE(15.3=100),PF0282614=2-Hacid_dh_C=FE(20.0=100)
A:
NA
C2:
PF0002516=Arf=FE(28.4=100),PF0282614=2-Hacid_dh_C=PD(21.5=56.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
TTGTCATCCTTGTGATAGATAGCAC
R:
GAGCACAGCAGCCCTGGATAT
Band lengths:
222-1213
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: