MmuINT0006137 @ mm9
Intron Retention
Gene
ENSMUSG00000056004 | 9330182L06Rik
Description
RIKEN cDNA 9330182L06 gene [Source:MGI Symbol;Acc:MGI:2443264]
Coordinates
chr5:9420617-9421657:+
Coord C1 exon
chr5:9420617-9420722
Coord A exon
chr5:9420723-9421504
Coord C2 exon
chr5:9421505-9421657
Length
782 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTT
5' ss Score
7.64
3' ss Seq
CTGTTTTCCTTTCCATACAGGGG
3' ss Score
10.85
Exon sequences
Seq C1 exon
GTAATGCTGAAATCAGGCACAAATATTCTGTACTGGAGAACGACAGGCATCCTTATGGGTTCTAAGGCAGTCAAGCCCGTGCTAGTAAAGAATATCACCATCGAAG
Seq A exon
GTATTTCATAGCTCTGTGCCTCAGGACTCGCTAGTCCAATTTTATTGTTAAAATATTTGTTAGACTGTTGGGTTAACTGACCTAAGTGTTTATAATAAAGACAAATGTCAGACATAATGCATGTCTAAAGATCTTAGTTTCATGTCCACCAAATTGATTAATCAGTTTTCTCTGTCCTGCCCTCAAACTGAATTATCTAATAGCTGTAAAGCAGAAAAGACAATAAATGACAGTCTTCAGTGTTTTTTTTAAAAATAAAATGGAAGTGGACTTGTGTACAAAAGCCCATTACTCATTAGAGGTATGCATATTATGCTAGTTAATCTGATCATTACTATATACATAAGAATAATAAGAATCTGGCTGTTTCCTAAACCTCTTGTGCCTTTCTGAGCCAGATGGGTCACTTTTGGTGCAGCTGAGCTACTAATAAACCCTATCATGGCTCCTTCTCAAGTAGGCTGTGTCTAGTCAAAGCAGCAATTCTTCTTCATTAAACTTTGGTATGTTTTGCTTATCCCATATGCCTGCTCCAGAGATGTTAACTCATTAGTCATTGGGACATCTGCTGGACCAAGCTGGGATTTCCATCCAGGAGCCATTACTAGGGTCATTCCTACTTGCTCACACACCATCAATCTTTCCTTGTTCCAAGTAGATAAGGACTGTGGGCTCAAGTTACTATTGTTCTTTCTGTCTTCTCTGCAGAAGCAACAAGTAGGTGCTAATGTGCTTATTGTGCTGGGTTCTCCCCTCTAAACCCTGTTTTCCTTTCCATACAG
Seq C2 exon
GGGTGGCATACACCTCAGAGTGCTTTCCATGTAAGCCAGGCACTTTCAGCAACAAACCAGGCTCATTTAACTGCCAGATGTGTCCCAGAAACACCTATTCTGAGAAGGGTGCTAAAGAATGTATTAGGTGTAAGGAGGACTCCCAGTTTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056004-9330182L06Rik:NM_172706:6
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:
PF076998=GCC2_GCC3=PU(0.1=0.0)
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=63.5),PF075629=NCD3G=WD(100=55.8)
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:
GTAATGCTGAAATCAGGCACAA
R:
GGAGTCCTCCTTACACCTAATACA
Band lengths:
249-1031
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: