MmuINT0026561 @ mm9
Intron Retention
Gene
ENSMUSG00000042507 | C130039O16Rik
Description
RIKEN cDNA C130039O16 gene [Source:MGI Symbol;Acc:MGI:2685106]
Coordinates
chr12:85500825-85501495:-
Coord C1 exon
chr12:85501429-85501495
Coord A exon
chr12:85500968-85501428
Coord C2 exon
chr12:85500825-85500967
Length
461 bp
Sequences
Splice sites
5' ss Seq
ACCGTAAGT
5' ss Score
10.43
3' ss Seq
CTGCCCTTCTACCCCTGCAGACG
3' ss Score
10.91
Exon sequences
Seq C1 exon
ATAGCTCTGAAGTCACCCCGCCTGTCCTCTCTGTGATGGGGGAGGCCACCCCTGTGAGCATCGAACC
Seq A exon
GTAAGTGCAGCCCCTGCCCCAGGCCCATGATGTGTGGGTGCCCAGGTGGGCCCAATGCATTGCAGATTAGCACTGGGTTCCCTGAGCAAGGGGAGGGTTCTGTGGGGCCTTCTTAGAGCCAGACTCTCTGAGCTTCTGTAGTCTATCCTGGCCTCTCTTGTCTTCTGCCAGCTTTTGTGTGGACGTTGCAGAGAGAGGGAAGGGAAGGAACAAGTTGGCTCGAATTTGTCATGAGGGAGAGCTGGGCGGGAGGGTCCAAGAGTCTCTCCTGATCTGTCAAGTATGGAGTCATGCCCCAGGCCAGGCTGTCTTCACTGTCTCCCAGAAGCTACATTCCCTACACCCAACTATGGCTTTACTGCACTCCGCATCTGCCAGCTGTACCGTTTTCTTCCCATCCTTGGGAGAAAATCAGGTTCTCACAGTGTGAGGCCTTACTCCCTGCCCTTCTACCCCTGCAG
Seq C2 exon
ACGAATCAACGTCGGGACCCGGTTCCAGGCAGAAATCCCCATGATGAGAGACCGAGCGCTGGCAGCTTTTGACCCCCATAAGGCTGACTTGGTGTGGCAGCCATGGGAACATCTTGAGAGCAGCTGGGAGAAGCAGAGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042507-C130039O16Rik:NM_001163502:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.261 A=NA C2=0.061
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0144819=ELM2=PU(79.3=93.9)
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:
ATAGCTCTGAAGTCACCCCGC
R:
TTGTCTCTGCTTCTCCCAGCT
Band lengths:
209-670
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: