MmuINT0138109 @ mm10
Intron Retention
Gene
ENSMUSG00000039656 | Rxrb
Description
retinoid X receptor beta [Source:MGI Symbol;Acc:MGI:98215]
Coordinates
chr17:34035654-34036454:+
Coord C1 exon
chr17:34035654-34035826
Coord A exon
chr17:34035827-34036324
Coord C2 exon
chr17:34036325-34036454
Length
498 bp
Sequences
Splice sites
5' ss Seq
AGCGTGAGT
5' ss Score
8.2
3' ss Seq
TCTCCCCCCTGTCTCTGCAGCCA
3' ss Score
11.74
Exon sequences
Seq C1 exon
CGGTTCAGGAGGAGCGTCAACGGGGGAAGGACAAAGACGGGGATGGAGATGGGGCTGGGGGAGCCCCTGAGGAGATGCCTGTGGACAGGATCCTGGAGGCAGAGCTTGCTGTGGAGCAGAAGAGTGACCAAGGCGTTGAGGGTCCTGGGGCCACCGGGGGTGGTGGCAGCAGC
Seq A exon
GTGAGTGATGGGATTGATTCTTTCTCTCCTGGGGTGGGGGTTGGGAGAAGGAGTCGGGTATGTTCCATCTCCCCTCTTCCCTTCTTTCAGTCCCTCCTTACCTTGCACTGAACTAAAAGGCCTTTCAATAATCTGAGGTGAGCCAGGTGTAGCGATCCATGCCTATAATGTCAGCACTTGGGAAGGGAGAGACAAGTGGATCTCCATGAGTTCAAGGCCAGCCTGGTATACATAGCAGGTTTCAGGCCAGTCGTGACTACATAGTGAGACTCTCTCTTAGAAAGTCTCGTCTCTGACACGGGGTGAAAGCTCCCTCTTCTCTGCTCCCATTGGACAGTCCCAGACTGGTAGTGGTTTCTATGACTGCCCTGAGAGGAGCCTGGACCGCAGAGGTGGATTGGATCCCGACAGGGAATGAGGGTGTAGAAAGGAGTATAAAACACCTCTCACAAGGAAGGTGTCCCCCCCTTCCCATGCATCTCCCCCCTGTCTCTGCAG
Seq C2 exon
CCAAATGACCCAGTGACTAACATCTGCCAGGCAGCTGACAAACAGCTGTTCACACTCGTTGAGTGGGCAAAGAGGATCCCGCACTTCTCCTCCCTACCTCTGGACGATCAGGTCATACTGCTGCGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039656:ENSMUST00000044858:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.828 A=NA C2=0.142
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=PU(0.1=0.0)
A:
NA
C2:
PF0010425=Hormone_recep=PU(23.5=97.7)
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:
GTTCAGGAGGAGCGTCAACG
R:
CCGCAGCAGTATGACCTGATC
Band lengths:
297-795
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types