MmuINT0138100 @ mm10
Intron Retention
Gene
ENSMUSG00000015846 | Rxra
Description
retinoid X receptor alpha [Source:MGI Symbol;Acc:MGI:98214]
Coordinates
chr2:27748612-27752441:+
Coord C1 exon
chr2:27748612-27748781
Coord A exon
chr2:27748782-27752311
Coord C2 exon
chr2:27752312-27752441
Length
3530 bp
Sequences
Splice sites
5' ss Seq
TCAGTGAGT
5' ss Score
7.68
3' ss Seq
ATGTCCTTTCTCCGTTCTAGCCA
3' ss Score
9.48
Exon sequences
Seq C1 exon
CTGTGCAGGAGGAGCGGCAGCGGGGCAAGGACCGGAATGAGAACGAGGTGGAGTCCACCAGCAGTGCCAACGAGGACATGCCTGTAGAGAAGATTCTGGAAGCCGAGCTTGCTGTCGAGCCCAAGACTGAGACATACGTGGAGGCAAACATGGGGCTGAACCCCAGCTCA
Seq A exon
GTGAGTGTCAGATGCTCACCTGCCTCGGTTTCCCCTGTACTCACTCTCTTACCCTCCTGCTTCAACAACCAATGAACCCCCAGCCCTTTGGCTGCCTGGCCTTTGTCCCCAGCAGTGAGACCTCTGTCCAGCTGGGTGGCCCTGTGAGTGTGGGGATACGCCAGCCTTCCTGCTGGCCTTGCTTGTCTGGCCCATCCAAATACGCAGCAGGGTCACTGTGGGATCTCGGCATACATCACGGTGAGGCTTGAGCTCAGTGCAGGGGAGTCCTTCAGAGAAGCTATGTGGAGCTGAGCTTGGGCAGAGCCCTCTAAGCTCCCTTTCCCACACACTGCTACAAGAAGGTGCAGAGGCCAACAGGGAGGTGCTCATCGCTCGTGGGTGGCAGCTGTTGTGACGACTGTTGAAGCAGAAGTGTCTCTTGGCCTTCAGCTGTCACCCTCGAGCTGGCCACCTGTAGGAATGGCCTAGACAATCATCTTCCCTCGTTTCCCTGTGCCACCTGCCATCTATAGCTGTCGTAGCCTCCAGACAAGACCGGAGGGCCATAGTTCCCACTGCTGGTTCACCTCCTGGCTGCTCGCAGGATCTTAGTTTCAGATCTTTCTGGCTTCCATGCCTGTTCCTGGACTTTCACCTGAGCTCTTCCCCCACTGTCCCCTGCCCTGCTCCTGCTGTCACTTAGGGGCCATTGGCCGGTGTGGATGTGTTTGGGTGGGGTACTCCATTTGCCCAAGGCCCCAGTGACGAGGCTACAGCCATGTCCCGGATTGGAACAGGGCCTTGCACAAACCCACAGGCCTCATGTTGTCTCAAGCTCATAGCCCAACTATGTCTGCCTCATATGAGCTTTTTATTGACATCCTGACCTCATCTGGACCCTCATGTAGGCTTCAGATCTGGGACCAGAGTCCTGCCATTAACCACTGGACACCCAGTCCAGGTAGACCTTAAGGAAGTCCCTTTCGGCTTCCCCCTCTGAAGCAGACTTAGCTAGTCTTCTCTTGCATCTTAGTACCCTCGTCTCAGCCTGTGACTGTGGTGGACACAGAGTACCCATTCTTTTCCTCCAACTCCAGGCACAGGGCAGCGGTATAGTGAGCTATCCCAGGAGTCAGTGGGGTGACTGAGCTCTGTGTTGTCAGGAGCCTTGCCCTGTCCCAGGGGCTCGGGCATGTCTCTTCCTCTCTGTAGTCTGTGAGCGGAGATCCCCCCTTGCATATTTGTGAGGACCCGTGACCCAGTTCCTATTCCCCCACCCCCACCCTGTTACCCAGCATTCATCTGTCTAATCCCAGAGCTGCCTTACTGCAGACAATGCCTAGGGCCTTGCAGGTGGTCTTCCTTGGGGGACCCAATCCTGGCCGTGTGAAGATAGCTCCCAATGGAGGGAGACCACAGAAACCCTTGCCCTCTGGAACCTGCCCAGTGCTCTGGTTGGCATCTGTTCCCTAAGCCCTCTTCCCAGTCCTGGAAGGGAGAGGAGAGCAGCAGGACTCGGCTTTGTGGACTAGGGCCTGAGGGTGGTTGGCTGGGGTCTGAAGGGTGACTAGGGTTTTCCTTTATCAAGTAAGGCCATTGTTGGGAATGGCCTCAGACGTGGCCTTAGCTGTTCTTCCATGAGGGTTCAGGTCTTTAGAGCGACACTGTGGAAAGCCTGTGTGCTCCAGTGTCTTGTGACTGGCCTTGATCTACATACATGGACCTCTCAGGCAAGCTGAGGAGGATAGGCTGCACCTAGCCTCACAGATGGGCTGCTGGCTCCTCCGGGTCCTGCCTGGGTGGTCTTGTGACCACGCCTAGCTGGCAAGTGGTAGCTCATTAAATGTCTGCTGTGGAGTCTGCTGAGAGGAGTGAAGCTACAGTGGAACGGAACAGGGCAGGACCAGAGTACTCTCAGCCCTCCCTTCCAGACAGCCCTCCTGTGGGTGCCTGCTGGGTGTGGGCCCTCACACCTACGTGGCCCCTGCCTCCTTCTTTCCCGGCTCCTCTGCTCAAGCCTTGTGTCCAGTCCTGGCAGACAGCATGTGTGTACATGGCCGCAGAGGCCACAGTCAGCCCCGGAATAACTTTGAGCTCTTTTTCCCAATCATAGTAGTATTGTGACACTGGATTCAAGAGGGTGGCGGCCAGGGAGAAAGCTGAGATCACAGAGCTTGGGTGTGAGGCTTGTTGTCTTACAGTCCGGTCTATGCATTCTCCCAGCTGGCTTAGGGCCCTCACTGTCTCCTGTCTTGGGGCTGCCTCCCCAGGAGATGGCAGGGAAGGAATACATCCACGGAGCAGCCCCTTGTGGCTGAGAGGCAGAGCCAGGCTGCAGACAGACAGTCCCTAGTACCTGTGGTGCCGGGGCTCCACTGGCCTCTCAGGTTTGCTGAGGGTTGTGTGGCTGGGAGATGTCACCCATTCCTTTGGACTCTGTCCTGGGGACCATGGGCTGCCGTCCCCTGTCCTTGCAGCCCTGGGCTTCCCTGCAGCCAGGCCTGCCAGGCCAGTGATGGGAAGCTGATTTGTCAGTGCCTTTCACTGAGCGCTTCACGGGCCCTTCACACGGGGCTGGGTGTTTAGACTGAACGTCACTGCTGAGCAGATGGTTTCTGTCAGCTGAAGGAAGCCCTTTAAAGCCGACAGTTCTCTCCTTATCGGATGCTTGGCTACTTCTTTTTTCAAAATCAGGAGTCTTGTATCCTGTTCTTGGGTACTCTTGCCCACCACACCCTGAGGTCAGAGGCTGTGACCCTGGCCCACCCGACAGGGTAGGCTTCCCAGCCTACTGTAAGGCCCACCTGAGTTCCTCACCTATAACAAGGCCTGGGTGTTCCTCTTCTGGGCAGAACTTTCTAGAAGGCTTCTGGTGATATCACCTCTACCTGCAACTTGGAATCCGGACCAAGCAAAGACCAGTCCAGCCCCAAGCTTGTACTTGCATGTTTGATAGGACTTCTCACCTGGGTGGCTACTGCTACCTTTAGAGATGGGGTCTGGCCCTATCTCAGCTCCCTCACCTTCCTGTTAAATGGCTCCTTTTCCTCTTCCCCCAGCACCTGCTCTCAGGGGTGGGGAAGACCTGATAGGCTTCCATGGTACAGATTACGTTTCCTTCAGCCATTGAGCTGTGTGACCCTAGTCTGTCTTGATGGGCCCCAGTCAGGTTTTGGGCAGCGCTGACTCTTATCTTCCTGCCTTTCCTGATTTGGAGGTTCCCCAGGCCCCCTGACTTGGGACTCCTGCCAGCTTCAGGTCAGCCATGTCCTCTAATCTGCTTTTCCTGATAACATCCCTTCTGACTTACAGCCTCCTGCTTCTTCTGATGACCACTGCCTTGGTACTAGTCCCGCTCCAATAAGCCAGGGCTTCCTCCAGCCTGTTACTATGGTGGATCTCTTCTCAGAGTCCTTTCACTGTGCCAGGCCTCCGATGGTTTGGGATGCAGATCCTGGGACCCCACTCCATGGGTGTTTTGTGTGGGGTGAGGTGGCTCTGTCGGCTATCAGGTGTGAGGTTTGATCAATGTCCTTTCTCCGTTCTAG
Seq C2 exon
CCAAATGACCCTGTTACCAACATCTGTCAAGCAGCAGACAAGCAGCTCTTCACTCTTGTGGAGTGGGCCAAGAGGATCCCACACTTTTCTGAGCTGCCCCTAGACGACCAGGTCATCCTGCTACGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015846:ENSMUST00000077257:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.579 A=NA C2=0.114
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=PU(4.7=15.8)
A:
NA
C2:
PF0010425=Hormone_recep=FE(22.4=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types