MmuINT0026562 @ mm9
Intron Retention
Gene
ENSMUSG00000042507 | C130039O16Rik
Description
RIKEN cDNA C130039O16 gene [Source:MGI Symbol;Acc:MGI:2685106]
Coordinates
chr12:85500600-85500967:-
Coord C1 exon
chr12:85500825-85500967
Coord A exon
chr12:85500704-85500824
Coord C2 exon
chr12:85500600-85500703
Length
121 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
AATGCTTCTGGTGAGTCCAGTGG
3' ss Score
-1.63
Exon sequences
Seq C1 exon
ACGAATCAACGTCGGGACCCGGTTCCAGGCAGAAATCCCCATGATGAGAGACCGAGCGCTGGCAGCTTTTGACCCCCATAAGGCTGACTTGGTGTGGCAGCCATGGGAACATCTTGAGAGCAGCTGGGAGAAGCAGAGACAAG
Seq A exon
GTAAGGAGAGATCTCCAGGGAGCAAGGCATGGCGGGCTGGTGGGCAGATGGGTGGGCTGGGTCCTGCAGGAGCCAGCCCTAACTTGATTTCCTGTTCTCCCAATGCTTCTGGTGAGTCCAG
Seq C2 exon
TGGATGACCTGCTGACAGCTGCCTGTTCAAGCATTTTCCCTGGGGCCGGCACCAACCAGGAGCTGGCCCTGCACTATCTGCATGAGTCCCGGGGGGACATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042507-C130039O16Rik:NM_001163502:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0144819=ELM2=PU(79.3=93.9)
A:
NA
C2:
PF0144819=ELM2=PD(19.0=31.4)
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:
CGAATCAACGTCGGGACCC
R:
CCCGGGACTCATGCAGATAGT
Band lengths:
235-356
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: