MmuINT0138105 @ mm9
Intron Retention
Gene
ENSMUSG00000039656 | Rxrb
Description
retinoid X receptor beta [Source:MGI Symbol;Acc:MGI:98215]
Coordinates
chr17:34168797-34169989:+
Coord C1 exon
chr17:34168797-34169168
Coord A exon
chr17:34169169-34169771
Coord C2 exon
chr17:34169772-34169989
Length
603 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TGTACGTACCCACTTCTCAGATT
3' ss Score
7.13
Exon sequences
Seq C1 exon
CCGAGCCGAGCGCGGCTCTTGAGTCGCGCTGCCACAGGCCGCGGCCTGCTCGCCTCCGCGGCTTCGTCGCGGCCCCCGAGTCCCCCGCTGTCCCCCCTGCGCGTCCCTGGCGCCTCTCCGGCTTCCCCGCCCTCGGCCCGGGCGTCATGTCTTGGGCCACTCGTCCGCCCTTCCTCCCGCCGCGGCATGCCGCGGGGCAGTGTGGGCCGGTGGGGGTGAGAAAAGAGATGCATTGTGGGGTCGCGTCCCGGTGGCGGCGGCGGCGGCCCTGGCTGGATCCCGCGGCGGCGGCGGCGGCGGCCGGAGAGCAGCAAGCCCTGGAGCCGGAGCCGGGGGAGGCTGGCCGGGACGGGATGGGCGACAGCGGGCGGG
Seq A exon
GTGAGTGTCCCGTGGGCCCGGGCCGGCGCCCCTCGCGCCCCCTCCCCGCGCTCCCGCCCCCTTGTTTGTAAACACGCGCCCTCGACGTCCCGAGGCCCAGCGCCCTCCCCCGGGGCGGGGCGCGGCGGGGGAGCTTCCGCCCTTCAGGTTCGGGCCCGCGGCGGGGCCTGCGTGCGCGGTCTCGGGCGTGGGAAGGACACCGTTCCCCGTGGGCTGGAGGACTCTGGGCATTCGAAGGCTGAGCTTACGCTCTGGGACCGGGTATTTCTGCCATACTCTTTGCCCCGAATGTTCTAAGTTGGGGTTGGACGAGGGGTTCGCTGCTACACCTCCACGTGCTGCTTCACAGCCCCCCCTCCCGAGGTCAGCTTGGGATGACCCAGTAGCCCCGCCTGACCTGCCTCCCTTTTTGTCAACCGCCTCCTCTCACGACTATTAGAAGTGAAATTGTTGTTTGGCCACTTGGTATTTCTGAACTCCAGGGTTGCGGGCTGTGGTGGGTCAGGGAGAATTAAAGTGTCCATTTGGATGATCAAAAGGCTCACTTTCTCTTCTTGTCTCTCCTGTCCGTGTGTGTCTGCCTTGTACGTACCCACTTCTCAG
Seq C2 exon
ATTCCCGAAGCCCAGACAGCTCCTCCCCAAATCCCCTTTCTCAGGGGATCCGTCCGTCTTCTCCTCCTGGCCCACCTCTTACCCCTTCAGCACCTCCACCTCCAATGCCACCCCCGCCACTGGGCTCCCCCTTCCCAGTCATCAGTTCTTCCATGGGGTCCCCTGGTCTGCCCCCTCCGGCTCCCCCAGGATTCTCCGGGCCTGTCAGCAGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039656-Rxrb:NM_011306:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.921 A=NA C2=0.805
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF118253=Nuc_recep-AF1=PU(62.9=90.4)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAGATGCATTGTGGGGTCG
R:
GACAGGCCCGGAGAATCCT
Band lengths:
356-959
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: