MmuINT0138101 @ mm9
Intron Retention
Gene
ENSMUSG00000015846 | Rxra
Description
retinoid X receptor alpha [Source:MGI Symbol;Acc:MGI:98214]
Coordinates
chr2:27607832-27609875:+
Coord C1 exon
chr2:27607832-27607961
Coord A exon
chr2:27607962-27609742
Coord C2 exon
chr2:27609743-27609875
Length
1781 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ATGCCTCACCCCTTCCCCAGGCT
3' ss Score
8.89
Exon sequences
Seq C1 exon
CCAAATGACCCTGTTACCAACATCTGTCAAGCAGCAGACAAGCAGCTCTTCACTCTTGTGGAGTGGGCCAAGAGGATCCCACACTTTTCTGAGCTGCCCCTAGACGACCAGGTCATCCTGCTACGGGCAG
Seq A exon
GTGAGTAGCCTGGGCAAGTGGCTGCTAGTGGATCAGTGGGCTCCTGCCCACTCCTGCATGCGGTATAGCGCTACCTTCCCCTTCCAGCTTAGAAAGTCAGTAAAGGGTCTCCTCGGCTGCCCGCCAGGTCTATGTGACCTCTGCAGCCGTGTCACCTTGGAAGCTTCAGGCTTTTTTCTGAGCAGAGGTCTTGATGCAAGTGTCTGGAGCATAAGAGTGTGTGTCTCTCATAGCCAAGGGGACTGTCGGGAAGGAGTGTAGCCTTGGAACTTGGGCTGAGGCTAGGTCTGTAGGCTGCCCTGGTCCTTATTGATTAACTGGGCATTGGGGCATGCTGACTGTTGCTCAGAGTCCACCAGGTCACCAGTAGGGGTGTTAGGATCGAGAGACTTAGATCGCCAACCTGTGGAGAGATGGGGATATATTGAGAATGTCACCTGCAACTCTTGCTCGCCACAGAACTGTGGTGACAGTTGACACTACCCCACTCCGGTGAAGAGCCCTGGAGACCATGCTGTCTCGAGGGGACTGAGTGCCCTGACTTGCTTTGGTTTTCTGCTTGCACCAAGGGCTCTCAGCCTCAGCCCACCCCAGTAGATACCATGAGCAGAGATGGTTCCCTGTTGTTTTGGAACCTATTTAGTTGGGGTGAGGCTCGCATGGGCACTGATCTTCCTAACTTCCCTTTGAAAAGACCTCTTGGTAGGTATGGGTTGCTGAGATGAACAAGATGGATCCTGCCATGTTTGCCTCTGCCTAGGTGGGCTTGTGGGATGGGGCATGTGAACACAGGACTTCTCTGAGGCTGGGAAGCACTGTTCAGGGGGAACTGCCACGGCTGTAGGAACTGCAGAGCCATCTGGCCTTCTCGCTTAACACAGGTGTCCCAGTGAGCACTTGCCACTGAGGCATGTCAACCCATGTAGAAGGGACAGCTCTAGGGTGGAGCCTCGGGTGACCTGCTCAGTGTGGGGCTCAGGTGCCTAGAAATGAGATGAGGCAGAATTGGCCCCACATATCCTTATGGGGACCCTGAGGTCACATTTCTGGGCGTGATCTCCCCTGTGGCAAGAAGCTTATCAGCAGGCCCCACTTCTCAAATGCTGACTGCTTCCATTTCCCATTGTAAAAGGGGTCGGTAGGCTTGGAGCCGGGATATGGGAACCACAAGGCTTGGGAAGTTTCTGGACCTGCTGAAAGGCTCCTGCCACCTTGTCAAGGAGCCCCTGGCTGTTTGTGCAGAGTTCTGTCTTCTCTCCCTCTTGAAGGCCCCTTTTTAGTGCTTTCATAGTAGCTCTGGTTGGTCGGTGCTGGGATGCATGGCACTAGGCCTGTGGTTCTAAGGTGGTCGTCCTCTCGGTACTCAACTCTCCTGGCATTCTGCATGCTCCAGACTGGCAGCAGTCACCTCATAGCTGTCACGGGGAAAGTCCTCAGGAGATCTCCCAGCTCCTCTGGGACACATGCATGCCCTCTTCATGTAAGAAAGAAGGTTCCATGCCCTGTGTTTGTTAGAGGGAGTCCTCGGGCAGAATTTCCCAGGCTGGTACATTGGTAGAATGTGTGCTTGCTAGAAGGAAGAGGCACTGCTCATGCTCAGGTGCTCAGGAATCTTCCTCCAGGTACACTTACTGGGGTCCCACTTTGAGGACCCTGACTTGAGTATGGCAGGAGATGAGTCTGGAGCATGCTGCTTCTGTGATCTGGCTGTGGGTGAGGGAAGGGACAGTGATGGGGTCATAGAAACAGCAGAGTGACCATATGCCTCACCCCTTCCCCAG
Seq C2 exon
GCTGGAACGAGCTGCTGATCGCCTCCTTCTCCCACCGCTCCATAGCTGTGAAAGATGGGATTCTCCTGGCCACCGGCCTGCACGTACACCGGAACAGCGCTCACAGTGCTGGGGTGGGCGCCATCTTTGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015846-Rxra:NM_011305:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.114 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(22.4=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(22.9=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:
CCAAATGACCCTGTTACCAACA
R:
CTGTCAAAGATGGCGCCCAC
Band lengths:
263-2044
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: