MmuINT0110545 @ mm10
Intron Retention
Gene
ENSMUSG00000026826 | Nr4a2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:MGI Symbol;Acc:MGI:1352456]
Coordinates
chr2:57110637-57112441:-
Coord C1 exon
chr2:57111576-57112441
Coord A exon
chr2:57110767-57111575
Coord C2 exon
chr2:57110637-57110766
Length
809 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TACATTCTCTCCCTCTACAGCGC
3' ss Score
11.08
Exon sequences
Seq C1 exon
CCATGCCTTGTGTTCAGGCGCAGTATGGGTCCTCGCCTCAAGGAGCCAGCCCCGCTTCTCAGAGCTACAGTTACCACTCTTCGGGAGAATACAGCTCCGATTTCTTAACTCCAGAGTTTGTCAAGTTTAGCATGGACCTCACCAACACTGAAATTACTGCCACCACTTCTCTCCCCAGCTTCAGTACCTTTATGGACAACTACAGCACAGGCTACGACGTCAAGCCACCTTGCTTGTACCAAATGCCCCTGTCCGGACAGCAGTCCTCCATTAAGGTAGAAGACATTCAGATGCACAACTACCAGCAACACAGCCACCTGCCCCCTCAGTCCGAGGAGATGATGCCACACAGCGGGTCGGTTTACTACAAGCCCTCTTCGCCCCCGACACCCAGCACCCCGAGCTTCCAGGTGCAGCATAGCCCGATGTGGGACGATCCGGGCTCCCTTCACAACTTCCACCAGAACTACGTGGCCACTACGCATATGATCGAGCAGAGGAAGACACCTGTCTCCCGCCTGTCACTCTTCTCCTTTAAGCAGTCGCCCCCGGGCACTCCTGTGTCTAGCTGCCAGATGCGCTTCGACGGGCCTCTGCACGTCCCCATGAACCCGGAGCCCGCGGGCAGCCACCACGTAGTGGATGGGCAGACCTTCGCCGTGCCCAACCCCATTCGCAAGCCGGCATCCATGGGCTTCCCGGGCCTGCAGATCGGCCACGCATCGCAGTTGCTTGACACGCAGGTGCCCTCGCCGCCGTCCCGGGGCTCTCCCTCCAATGAGGGTCTGTGCGCTGTTTGCGGTGACAACGCGGCCTGTCAGCACTACGGTGTTCGCACTTGTGAGGGCTGCAAAGGTTTCTTTAAG
Seq A exon
GTGAGCAAGACAGGGCGGAGGTGGCAGGTAGCGGTCCTTATACCTGAGACCCAGCAGTGTACCCTCACCTTCCGGTCGGCAGCCCCGCTCGAGTTCCCTGCAGCTACTCACAGGCTGTGGAAGAGGCTTTGGGGGTGTCTAAGGAAAGAAATCAGAAAGACTGGTAGAGTCAGGGTTTCATCCCCCCGCCCCCCGCGCCCCACAGCAACCTGCGGCCCCGGCGGGCTCCAGCCCGAAATTGCTGGAGCCAGAGTTGGAAGAGGGCTATTTGCATGTGTTAGGCGCTGTCTTCCTTGTTCAGATTGAAATTGGTTAGGACAGAGAACCGTGTCTGAGCTAACCAAGTGGAACAGAATTCCCTATGGTCAAATTAAGTGATCTCTTTATTTCGCCATCCTGATTGAATAATCTTATCATTTTAAATAGAGAAGGTCTCCAAGGAATGTAAATAATATGAATGCCCACGGATTTGTATTTACTGAGCGTCTCCTGCCCCTTCTCCTGGCATATAAAACACAGCAAGGAGCGGTAAGGTTAGCTCAAATGTTAACGCTATCAATTTTCTTCTGGTAAATGCCCTGGGGAGGAAAAGGAAAGGAAATAGGAAGAAAAGAAAAAGAAAAGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAATTGAAGGAGTAGTGTTTATGTTTGTAGGGAAGGAATGCAGATCCAAGCCATTTTTTAAAAAAATGTGTCCAGTTTGCTGGACTTTGAGTGAAAAAAATAATCATTTTGGGGCCTACATTCTCTCCCTCTACAG
Seq C2 exon
CGCACGGTGCAAAAAAACGCGAAATATGTGTGTTTAGCAAATAAAAACTGCCCAGTGGACAAGCGCCGCCGAAATCGTTGTCAGTACTGTCGGTTTCAGAAGTGCCTAGCTGTTGGGATGGTTAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026826:ENSMUST00000112629:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.529 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(38.6=12.0)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
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:
TAGTGGATGGGCAGACCTTCG
R:
CCCAACAGCTAGGCACTTCTG
Band lengths:
347-1156
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