MmuALTA1004546-2/2 @ mm10
Alternative 3'ss
Gene
ENSMUSG00000015846 | Rxra
Description
retinoid X receptor alpha [Source:MGI Symbol;Acc:MGI:98214]
Coordinates
chr2:27741764-27748671:+
Coord C1 exon
chr2:27741764-27741943
Coord A exon
chr2:27748612-27748619
Coord C2 exon
chr2:27748620-27748671
Length
8 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
TGACTGTCTCCTGTTTACAGCTG
3' ss Score
10.63
Exon sequences
Seq C1 exon
GCAAACACTATGGGGTATACAGTTGTGAGGGCTGCAAGGGCTTCTTCAAGAGGACAGTACGCAAAGACCTGACCTACACCTGCCGAGACAACAAGGACTGCCTGATCGACAAGAGACAGCGGAACCGGTGTCAGTACTGCCGCTACCAGAAGTGCCTGGCCATGGGCATGAAGCGGGAAG
Seq A exon
CTGTGCAG
Seq C2 exon
GAGGAGCGGCAGCGGGGCAAGGACCGGAATGAGAACGAGGTGGAGTCCACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015846-29-13,29-12-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.579
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(82.9=95.1)
A:
NA
C2:
PF0010425=Hormone_recep=PU(4.7=15.8)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGTACTGCCGCTACCAGAA
R:
CACCTCGTTCTCATTCCGGTC
Band lengths:
92-100
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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