MmuINT0138106 @ mm9
Intron Retention
Gene
ENSMUSG00000039656 | Rxrb
Description
retinoid X receptor beta [Source:MGI Symbol;Acc:MGI:98215]
Coordinates
chr17:34169772-34170656:+
Coord C1 exon
chr17:34169772-34169989
Coord A exon
chr17:34169990-34170499
Coord C2 exon
chr17:34170500-34170656
Length
510 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCCTGTCTCCCCCATCCCAGATC
3' ss Score
9.57
Exon sequences
Seq C1 exon
ATTCCCGAAGCCCAGACAGCTCCTCCCCAAATCCCCTTTCTCAGGGGATCCGTCCGTCTTCTCCTCCTGGCCCACCTCTTACCCCTTCAGCACCTCCACCTCCAATGCCACCCCCGCCACTGGGCTCCCCCTTCCCAGTCATCAGTTCTTCCATGGGGTCCCCTGGTCTGCCCCCTCCGGCTCCCCCAGGATTCTCCGGGCCTGTCAGCAGCCCTCAG
Seq A exon
GTGAGAGAGAGGTTGTGGCCTGCTTATTGCCACTGTGCCTTCAGTTCCTTGTTCTCAACTTCTCACCCCCACTCCCCATCTTTGGGTGAACTTCCCCAAAACCCGTTGATCTTTCTAGTTCTCTAATCATAGCAAGCCTGTGGTCTCGGACCCCTTGCTCTTCCTGAAGGGGGTGGTCTGTGGGGGTGCATGCTTCATCAGCTCTGTTTTGAAAACAAACCCTAAGCCTGCAGGGAATATTTTTGATGTCCTGTTCAGCTCACGGTGGCTTTGCTGCCCTTTTCGCTTCAATATGCCTGCCCTTCTAAGACCTGTGCCCTTCAGGGCCACTGTAGCACAATTACAGAAGGGTGGACATCACTCTTGGTGTCACGTGCAAGGAAGGCCCTTTACGTTAGACAGTAGTGTCCCCAGTACCTTCTGGAATAGTACAGGGCTTGCTCACAAGCAGGAAGTGGTTTGCCTGACATATGAGAGTCTCCTGTGACTTCCCTGTCTCCCCCATCCCAG
Seq C2 exon
ATCAACTCCACAGTGTCGCTCCCTGGGGGTGGGTCTGGCCCCCCTGAAGATGTGAAGCCACCGGTCTTAGGGGTCCGGGGCCTGCACTGTCCACCCCCTCCAGGTGGTCCTGGGGCTGGCAAACGGCTCTGTGCAATCTGCGGGGACCGAAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039656-Rxrb:NM_011306:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.805 A=NA C2=0.628
Domain overlap (PFAM):
C1:
PF118253=Nuc_recep-AF1=PU(62.9=90.4)
A:
NA
C2:
PF118253=Nuc_recep-AF1=PD(35.2=69.8),PF0010513=zf-C4=PU(15.7=20.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGACAGCTCCTCCCCAAATCC
R:
CAGATTGCACAGAGCCGTTTG
Band lengths:
345-855
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: