MmuINT0138122 @ mm9
Intron Retention
Gene
ENSMUSG00000015843 | Rxrg
Description
retinoid X receptor gamma [Source:MGI Symbol;Acc:MGI:98216]
Coordinates
chr1:169564566-169565936:+
Coord C1 exon
chr1:169564566-169564657
Coord A exon
chr1:169564658-169565830
Coord C2 exon
chr1:169565831-169565936
Length
1173 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
CAATCCATTGCTCTCTGCAGATG
3' ss Score
8.01
Exon sequences
Seq C1 exon
AGTCCTTACAGAGTTGGTGTCCAAGATGAAAGACATGCAGATGGATAAGTCAGAGCTGGGGTGCCTACGGGCCATCGTGCTGTTTAACCCAG
Seq A exon
GTAATGTCTGTTTAACTCCAGCCACTGTGTGGGGCTCAGCCCTCTCTCAAGGTTGACCTCTGGGGCTCTGATTTGCTCCGCCCCGTCCCCCACTTCTAAGCTCAGCGGAGACAGAACAGTCTGAGTCCAGAAGCCATCAGTCTATAGAGTCTTCTCTTCATTGCCTCTCCTCTCCAGAGCCATTGGTATTTCAGCTGGGTGTGGGGTTTCACTGGGTGGGAGCAGCTGGGGTGGATGAGATCTTCTAGTGAGCTGGATGTAGGGTATGGAAGAACGACAAGTGTCATATATGTCTCAGGAGTGTCATATATGTCTCAGGAGTGTCATATATGTCTCAGGAGTGGTTCATTTCCCATTCACTTGGCATGGGTAAAACTCCAGGGCAGCATGTTCTAAGGGTGAGTGGGTTATAACCGGGATGTTTTCCTTGGACAATGAACTTGGGGGGATGGACAGTAGACATGCAAGAGAAGCCAAGACCAAAGATACTTAGGTAAGAGCTGGCCTCCTCTGCCTGAATTGGGAGGCAGCTGTGAACCTGATGGGACATCACTTGTGAGCAAAGACAGCAAAAAGAGCTGGGTACTGAGAATCTCACAGGCTGGTGGGAGAAAGAAGGGCTCTCAAAGGAGCCTAGCATGCGGTTAGTGGGAAGGAAGTGGCATCTTGGAAGTCCAGGGGCAAAAGCACTTTAAGAGGAGGAAGTGACTAGCTTTGTCAAATGCTGCTGGGTATGTCCAGTCTTCAGTAGTTTGACATGACAAACGTAAACCCTTTAGGTCCAAGACTGATGTAGCTATGATGCGGTCCATGTGTAGGGTTTGCTTTCGTGCCCCATCTCAACACTTAGGCACACTCGGCGTGTCAAAAGCATCCGGTGAGGGCGTGAATATTGCTTTTCGAGACAGGCCTGGATAACCTCTCCTTAAGTCAGCAGAGGGTCTGTTTCACTATTGATATTTTAAAATCCTTCAGATGGAGAGTTTGTTAGGGAAATGACGCACAGGAAAGATAGCCACCCGACGCAGGGGATCTGTTTACTTCCCAGTTGTGCCTGTGAGTGAGTTCCAAGTGTCTCTCACAGCCCCAAGGGAGGTGGCCAGTTTGATGCTGTCTGGAGGAGGGTGTCCTGCTGAGGCATTAACCAGAAATTCAATCCATTGCTCTCTGCAG
Seq C2 exon
ATGCCAAGGGTTTATCCAACCCCTCTGAGGTGGAGACTCTTCGAGAGAAGGTTTATGCCACCCTGGAGGCCTATACCAAGCAGAAGTATCCGGAACAGCCAGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015843-Rxrg:NM_009107:8
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:
PF0010425=Hormone_recep=FE(16.1=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(18.1=100)
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:
AGTCCTTACAGAGTTGGTGTCCA
R:
CTGCCTGGCTGTTCCGGATA
Band lengths:
198-1371
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: