MmuINT0138110 @ mm9
Intron Retention
Gene
ENSMUSG00000039656 | Rxrb
Description
retinoid X receptor beta [Source:MGI Symbol;Acc:MGI:98215]
Coordinates
chr17:34173270-34173702:+
Coord C1 exon
chr17:34173270-34173399
Coord A exon
chr17:34173400-34173569
Coord C2 exon
chr17:34173570-34173702
Length
170 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGT
5' ss Score
8.02
3' ss Seq
CGGTGCCTTCTGGCCCCCAGGCT
3' ss Score
8.15
Exon sequences
Seq C1 exon
CCAAATGACCCAGTGACTAACATCTGCCAGGCAGCTGACAAACAGCTGTTCACACTCGTTGAGTGGGCAAAGAGGATCCCGCACTTCTCCTCCCTACCTCTGGACGATCAGGTCATACTGCTGCGGGCAG
Seq A exon
GTTAGTGATCTCTTTGAACCCTCTCTAGTCTCTTGACCTTCACTGACCCCAGCAGCGTTCTCGTGCATATTCAGGGAGCCCAGCTGGCTACCTTGCCTCTGTTTTCTTTGTACTTGGGTTCCCGTGGCCTGGTGTCCGGCTGCTGACCCTCGGTGCCTTCTGGCCCCCAG
Seq C2 exon
GCTGGAACGAGCTCCTCATTGCGTCCTTCTCCCATCGGTCCATTGATGTCCGAGATGGCATCCTCCTGGCCACGGGTCTTCATGTGCACAGAAACTCAGCCCATTCCGCAGGCGTGGGAGCCATCTTTGATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039656-Rxrb:NM_011306:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.136 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(23.0=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(23.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGACTAACATCTGCCAGGCA
R:
CGATCAAAGATGGCTCCCACG
Band lengths:
251-421
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: