MmuINT0138104 @ mm10
Intron Retention
Gene
ENSMUSG00000015846 | Rxra
Description
retinoid X receptor alpha [Source:MGI Symbol;Acc:MGI:98214]
Coordinates
chr2:27757761-27762957:+
Coord C1 exon
chr2:27757761-27757866
Coord A exon
chr2:27757867-27759540
Coord C2 exon
chr2:27759541-27762957
Length
1674 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TACTCTCTCCTGTCCTGCAGGTT
3' ss Score
11.29
Exon sequences
Seq C1 exon
ACTCTAAGGGGCTCTCAAACCCTGCTGAGGTGGAGGCGTTGAGGGAGAAGGTGTATGCGTCACTAGAAGCGTACTGCAAACACAAGTACCCTGAGCAGCCGGGCAG
Seq A exon
GTGAGCCCCGCCTCCATCTTGGACAGCCCCCTGCCTCTACCCTTGGGCTCAGCCACACATCTCCAAAGCCCTCTGTATGCCACAAAACAATGGTGTCCTCCTTAAACCAGCCTGGGGTGCTTTTCAGGCTTTGAGCAGGAGCTAGGCAGCCCTTGGACTCATGAGCTCTGAGGACTACCCACTTCCCCCTATACCCAGTTGAGATAATTGATCCATTTCTTAGTGCACAGTAGGTCCTTGCTATTTACGAGTATGAAGCCTTATGTTCTTCACCTGTTACGTGACCTGGAAATGCCAGCACAGCGTAGGTGCTGTACAGTTGTGCATAATACGTGGCTGAGACTGGAGAACACATTCTTTCTGCTGGCCTAAGGAAGACTGGCATCTAGTCATGTTCAGTGCTGGGTGCACAGTCTAGTGTTAGGCACACAGTAGGTGTCCAGGAGAAATGGTGTTTTCCAAGGATTCAGTTCTGCTTCTTCTTGCAGTCTCCCAGTGTGCAGGCTAGGTGTGAGTGGAATAGTGGAAGACCGGGGAGATGGGCACACTAACCAATCTCGTTGCCTGGCACACACATGGTTAACTGTCCACACTGCTGTTTAGCCCTCATCTGGTTTGGTTTAAAGTGAAACTTCCCGGAGGAGGACAGGAGGGTGGCAGCGGCTTGTTTTTCCTGGCTTCCTGCCTTAGCCCATCTCGCCAGCTCAGCAGAAAACAGCCTGTTCTCTGGCACCTCTCCAGCCTCCAAGCTACGCTTGTGCCTTTAAACTGAGGACTGCGGGGCAGCCAGCCACAAGGCTTCCTCCCTGGAAATGAAAGACATTGTTAATAATTAATGAGGCCCAGAGCCCCCTCCAGTATATAGGGAGGCCCTGAGCAGACACAGAGGTCACACGTGGGACCCCAGGTCCTGTCCCCACACCACACTGTCCTCTCTTGTCTGTCCACCTTCCATGAGTTCTCAGATTCCTTTCCCATGCCTATCGGTCTTTTGCCCAGGAAACATTCCAGGGGTAAAGGAACCCAAAGGCCTCTGCGGTCCTCTCCAGGGAGGTGCTCCTGCTGAAGCAGGGGATCTCCCAGCTCACTGCTGGCTCCACTGTCAGTCACCCCGAGTACCATGCGTGTGACTGACTACCAGTCAGGCTGCCCACAGAGCTTCCTGGTGCCTCTTCCTAGGACATGCCCCACTGCCTCTAGCGAGACAGCCGCTCTTGCAGAGGCCTCTCCGATGCACAAAACATGTTCATGCTCTTACCTGCCGAAATTTCTATCAAGGCTCCCCGTTGCCCGTGGAGCAAGCCCACACTCGTAACTGCTCTCCCAACCCCTGCCAGGCCTGTCCTGGCCGACAGTAGTCAAGCATTGGCTCTTCCTTTCATTTTAGGATCTTGATGCAACTCAGCCTGCTGCACCCCTGCCGCACCCCCACTCCACCCCTGCCACTCCTCTGCCCCTTGTGCTCTTTTGTCTCCAAGGAGCCTCCTTTCTCTAGTCCCCACTTCTTCCTGGAGCATCAGTTTAGGCAGTTTCCTCTGCAGACCAGGTTCTGGTCCCAGGCACTGGGCTTGGCTGGTCTCCGGGGAAGTTACAAGTCACCAGGTAGAGCAGGGAGCACTCCGAGGGGAGCATTCCCTGCCTCCTGGCCTGTCCTTACTCTCTCCTGTCCTGCAG
Seq C2 exon
GTTTGCCAAGCTGCTGCTCCGCCTGCCTGCACTGCGTTCCATCGGGCTCAAGTGCCTGGAGCACCTGTTCTTCTTCAAGCTCATCGGGGACACGCCCATCGACACCTTCCTCATGGAGATGCTGGAGGCACCACATCAAGCCACCTAGGCCCCCGCCGCCGTGTGCCGGTCCCGTGCCCTGCCTGGACACAGCTGCTCAGCTCCAGCCCTGCCCCTGCCCTTTCTGATGGCCCGTGTGGATCTTTGGGGTGCAGTGTCCTTATGGGCCCAAAAGATGCATCACCATCCTCGCCATCTTTACTCATGCTTGCCTTTGGCCCAGGGCCATAGCAGAGCTGGTGTGACACCTGGCCAGCTCCTGCCCTACATCAGGCTCTAAGGCTATGCTGCTGTCACCCCGAGGGTCGTGGGGTTCGTCATGGGGCCTTCAGCACCTGGAGCTGCAAGAGCTGGGAAAAGGGCTTGTTCTGGTTGCTGGTTGCTGTCGCTGGTTCTCGACATCCCACATGGCACCTCTGTTTGGAGTGCCCCATCTTGGCCTGTTCAGAGTCCTGGTACCCAGTTAGGGTGGGAATCCACCTGGGATCAAGAAGGAGCAGGTGGGGCAGGCCGTATCCTCCTGGGTCATAGCTAACCTATAAAGCCTCTTTCCAAAGATGCCCTGAGATATCACTCCAAGCAGGATTCTGGGACCACCTTGAGGCTGCGTGGGCTGGAGGTCCTCTGTCATGTCCCCCAGTTGACCAGTTCCTTTTTATGTCATCGTCCCTCTTCATGTCTCACCAATCCAGGGTTAGCCAACTATAGTAGCCTGGCTTTTCCCTATCACAGATCTTCCTTTCTGGTCTTCAAGATGGCACCACCAATCATCCTGGAGGGCTGCCCTGGCTCACGTAGAGTGGGGTTTCCACTTCAGTGGTCCTGTGGGACACTGGGCATCCTGAGGCTCAGGGAGGAGAGGAGGGCTGTTGTCTGGTTTTGGGGAAGGTGGCCTGAGGGACTTGGAGCTGAACCATGAAGGCATGGCAGGTGGCTGTCCTGGTGTGACTGAGTCAACAGGCTCTGTGTGGGACTCTAGCATGGGCCCTTTCTCGGACTGGCCACTTCTGTTAGAATCCTGACAGACAGGGACTTTCTGGGACTTCTTTTGGAATGGTGGTGTCTGTGGACAGTGTTTGCTCAGAATCTGACCCAATGGTTCTGTCATGCCTGCTCAGGTGGCTGGCTGCAGACTCAGGCTTCAGCCCTGTCCCATGTGGCTCTTGAGTGTGCCTCTCCAGTTGACCAGCCTTGTTTGCACTGTGGAGCCTCCTTGGGTGTCAGTCTTCATGATCTAGTCTCAGACTCCAGGGCCCAGGCTTGTCAGGAGCAGGTGCCTTAGTGGGTGTGGCCATACTGCCTCCCCTGTAGCTGGTCTCCCATGAGGTAGGAGGGAGAAGGTCCTCACAAAACAGACCACCTAGGGGATTGGACCTAGAGGTGGTGGGTGGGAGGGTCCAGTTTCCTGGGCTCTGCGGGGAAGGACACATTGCTTTTCCATCTTTTCAAAATCCTAAACCATAACCGGCAGAGGCACCCATAAAAGATTCCAGAAACATCTTCCCTGTATCCCTTCTCTCCATGTAGTGGCATGGGAGCTGACCGTGGAGACAGCACGGTTCCCAGGACCCGCTGGCTGCCCCTTTCCTAGGCTTTGCTAGAAAATCCGTACAGCCTTTGGGGCTAGTAGCATCAGGCGGAGGAGCGGATTCCCTAGTCCATACCCAGCACCGTGCCTTCTGCAGACCCCCCTCTTCCATTGTTCATGCCAGCCCCATTCCACACTGTACCCTGTCCCTCTGAGCCACAGAGAATGCACAGTGGCTCCAGCAGAGGAAGTCCTGGGGCTGAGCCATGTCTGGGCTTGGCTGGCTGTCAGGCACTGGGGCCTTGGCCGAAAGCCCCACTGGCCCACATAGCCTTACCTGCCACTGCTTGTCACTATAGATTCCCTGGTGAGCTTCCTGCTCCTTTGGCCTCATTGTCACTGTCATGGGGGCAGTGTTGCTTGTTTGCAATGGTGGTGTGGGCGTGGTGTCACTAAGGAGAAAATTGGAGCTTCATTTAACCAGACCTTCAGTCGTGTTACCAATTTGGCTCAATTAAGGTGATTGTAATTATTATTGTTATTATTTTGGTGGAACAATCTTTAATTTTCTAAAGATAGCTCTAACATCAGCTCATTAGCCACCCTGCGCCCATCCCCACCTCAACCTGATTGGATTGTTGCCACCAATGGTCATGTGACTTCCACATTGCAGCTTCTGGGCCATATTCCTCATGTGTGTCACCACCCTGCTTGGAGATTCATCTGGGGCTCCTGTGGCCGAGAAACGAAGATGACCACAGGGCCTGTGGCAGCTGCTGGCCTGTGTCACCCTGAAACAGTCACTGGGGGAATTTGGCCCCCACGCCCTCAATTTTCCAAATTACAGCATCCCCAGGATCCTGGGCAACTTGGTGACAGTGCCAAGAGACACCCAGCCCCCCTCCCCTGGCATCCCAGGATACCTGGCGAAAGCAGGCAACCAATGGCTAGTCATCTGCTGTCCCCGTTGTAGAACTGGGGCTTGTGACCGGGTCTCCATGCACACGTGTATGGTGTGAACACATGTGCTATACAGAGACTGCCCACTGACGACGGGAGATGCGGCACAGTTACTGGTGTTTTGTGTTCTTTTTAATCAAGACTTTCCCATTTTCCTGTACATTTGCTTCTCGTGAGCAAGGACCTGAGGTCCCCTTCTGTGGGGAAGTCGGGCTCTGGGGACTCTCTGGAGGCAGGGGATGCATCTATTTTCAGATGCTTCAGGGCTGGAGTGCCCTGAACTCTAGCCATGCCTTAGCTGGGATGTGCGGCCACCATGGGGAGGAGGCCGCGTCCGCAGGGAGTAAAGATAGAGGAATGTTTAACGCACCGGGAAGGGTAAATGAATCTATTTTTGTACAAATGTAATTTTATCCCTCATGTAAACTGGATGGCATGGTGGGGGACCTATTTTGTTTCTGCTTTGAGTGTCAAAAACTGTTGGGACACCCTGACGCTGAGACAGCAGAGGAGGCGCTTACCAGGCGGCTGAAGGCGTGAGAACAGCACAGACAGACACTTCCTTCGGTGGGAGGGGGGCCGCACGGGCAGGGTTTCCTTCCCCTTCTTGGTGATTTGAACAGCCCTGCTCTGTCCTCGGTGCCTGCCTGCCTGCCTGCCTGCCGGCCTCTGACTGTGAACTGACTCCCCACGGAACTACTCACTGGGACATTGTGGTGCAGACGCCGGGGGGTTGATGAACAGCAGTCTCAGGATTATAGAAAAGAAACAACAACATGAGAGGAGAGACAAATATGAGCGTTTCAAAATATATCTCCATTCGGTTCTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015846:ENSMUST00000077257:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(18.2=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(14.6=56.0)
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:
AGGGAGAAGGTGTATGCGTCA
R:
GCGAGGATGGTGATGCATCTT
Band lengths:
357-2031
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