MmuINT0138103 @ mm9
Intron Retention
Gene
ENSMUSG00000015846 | Rxra
Description
retinoid X receptor alpha [Source:MGI Symbol;Acc:MGI:98214]
Coordinates
chr2:27611719-27613386:+
Coord C1 exon
chr2:27611719-27611810
Coord A exon
chr2:27611811-27613280
Coord C2 exon
chr2:27613281-27613386
Length
1470 bp
Sequences
Splice sites
5' ss Seq
CTGGTACGG
5' ss Score
8.6
3' ss Seq
GAGGCTATTTTTCTCTACAGACT
3' ss Score
6.83
Exon sequences
Seq C1 exon
GGTGCTAACAGAGCTGGTGTCTAAGATGCGTGACATGCAGATGGACAAGACGGAGCTGGGCTGCCTGCGAGCCATTGTCCTGTTCAACCCTG
Seq A exon
GTACGGTCCTCCTGCCTCCCACCTGGCCAAGAGCATGCGAGTCTTCCCAGCTGCTCTGCGCCATGCTTTGACCTTCAGGGCCCAGTGTCCACATTACAACAGACACCAATCTCCTGCCTCCACTTGTCTGGAGATGTAATGGAGAGGCTCAAGTGGCACTCTATGCGGCCAGAGTAGGCACTTGACATTAGTGCTCTCCAGCTGAGCCTCGTGGGCTCTGCTGTCCACAGTGGTCTAGTGTTAGAGTGAGCTCCCAGGATGGGGTTGGTGGTCAGTTGGTCAGTCCATCTTGTTAGGTGTCCTGAGGGTAGCTAACTTGTCTCAGGCCTTGGCTTCAAGGATATTTGGGGACAGGGCAGAGCAGCCTCTTGAGGACAGCAAATCTTTTTGGTAGCTCTGGAGCTGCAGTGTTCAGGGCCTCCAAGCTGTTGCTGTCACAGAGGCCGAGACTGTCTTCTGTGTGGGAGGCTGTGGTGTGAAGAGTGGCCCAGGCCTGTGCTCACAGCACTGGGTTGGTGGCAGATGCCACTGGTGGCCAGTCCACATGGTGATGGGAGCACACAACTGAGAGCGTGGAATTCTTCCTGGGGAGAAATTCAGGGATTCAAGAGATGGCTGTGGGCTTGTGGGTGGCTCTGACTAGGCTCCAGGAAGCCGCGGAGGCTGGAGCACTCGCTGCCGCAGGGTATGCATGGGCTTCTGTATTTGAAAGTCCATCCTTGTCTGCCAGGGGAGGGGTTGAATATGGGTTGGAAGCTTGGCTGACGGGGCTCACCAGCCCTGCACATGGTGAGTAGAAAATATGGGGGGACAGGGATATAGGCTTCTACCCCAGATAGCTCATTCCTGAGCCAACCTGATAGTTTCTCAGGTTAGGTCTGAGTGGTCTGGCTGGAGGCATGGTGAACCAGGGAGGCCTCAGCTGGGGCTCCGAGGGATAGGGAGGGACTGTCAGGGACTAGATCAGTTGAAGGTGTCTTGTGTATTCTAAAGAGCTCCCAGACCCCAAAGTGCCCTCAGCATTCTTACTGGTACACTGTGCCCTGATGGTGTTAATGACTATGGCTGTGGTTTTTCTCTAGCCTGTATTGTGGCCAGTGTTTAGGCGCTGAGGAGGGGTCTCCTGGCTCATGGTATGGGGAGATCCTCAGGGAAGGGCTTACAGCTTTCTTCCTGTCATTGGGACCAGGCCCAAGGGCAGTGAGAGGATTGGTTATCTCTCATGACCACCTGGAGAAAGATGGGGAAACTAAGTCCCTGAATGACAAGGTACTGGTTTAAGGTCACTTGACTTTCAAGTGGCCGAATGGAGACATAATATGACTCTAGAACACCCATCCTCCTGGTCTGGGAGCTATGGGTCTGCAGGGCAGCCATATCTAGTTGTGTAGCATGCACACTCTCTGCTATGCTTGCATGTGGATAGGAGATAGTCTGGGGGCTCTGACCTGAGGCTATTTTTCTCTACAG
Seq C2 exon
ACTCTAAGGGGCTCTCAAACCCTGCTGAGGTGGAGGCGTTGAGGGAGAAGGTGTATGCGTCACTAGAAGCGTACTGCAAACACAAGTACCCTGAGCAGCCGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015846-Rxra:NM_011305:8
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(18.2=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:
CTAACAGAGCTGGTGTCTAAGATGC
R:
CCGGCTGCTCAGGGTACTT
Band lengths:
190-1660
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: