MmuINT0110538 @ mm10
Intron Retention
Gene
ENSMUSG00000023034 | Nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:MGI Symbol;Acc:MGI:1352454]
Coordinates
chr15:101270083-101271865:+
Coord C1 exon
chr15:101270083-101270969
Coord A exon
chr15:101270970-101271735
Coord C2 exon
chr15:101271736-101271865
Length
766 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTT
5' ss Score
7.64
3' ss Seq
CGTGTCCCCCCTTCCTCCAGCGC
3' ss Score
10.98
Exon sequences
Seq C1 exon
AGATGCCCTGTATTCAAGCTCAATATGGAACACCAGCAACGAGCCCAGGACCGCGTGACCACCTGACCGGTGATCCCCTGGCCCTTGAGTTCGGCAAGCCTACCATGGACCTGGCCAGCCCCGAGACAGCACCTGCCGCACCTGCTACACTGCCCAGCTTCAGCACCTTCATGGACGGGTACACCGGAGAGTTTGACACCTTCCTCTACCAGCTGCCGGGGACGACCCAGCCGTGCTCCTCAGCTTGTTCCTCTGCCTCCTCCACGTCTTCTTCCTCATCCTCGGCCACCTCCCCCGCTTCGGCGTCCTTCAAGTTTGAGGACTTCCAGGTGTACGGCTGCTACCCGGGCACCCTGAGCGGCCCATTAGATGAGACCCTATCCTCCAGCGGCTCTGAGTACTATGGCAGTCCCTGCTCAGCCCCCTCGCCATCTACACCCAACTTCCAGCCGTCCCAGCTTTCTCCCTGGGACGGCTCATTTGGCCACTTCTCCCCGAGCCAGACTTATGAAGGCCTCTGGGCATGGACAGAGCAGTTGCCTAAGGCTTCTTCAGGGCCTCCGCCACCTCCAACCTTCTTCTCCTTCAGTCCTCCCACTGGCCCCAGCCCCAGCCTGGCCCAGAGTTCTCTGAAATTGTTCCCACCACCAGCCACCCACCAGCTTGGGGAGGGGGAGAGCTATTCCATGCCAGCAGCTTTCCCCGGCTTGGCACCCACCTCTCCGAACCGTGACACTTCCGGCATTCTGGACGCACCCGTGACCTCCACCAAGTCCCGGAGCGGGGCTTCAGGTGGCAGCGAGGGCCGCTGTGCAGTCTGTGGTGACAATGCTTCGTGTCAGCACTATGGGGTCCGCACCTGTGAGGGCTGCAAGGGCTTCTTCAAG
Seq A exon
GTATTTTGTTGGTTCTGGGGGACGATGATATCATGTTGGAGGTGGGGGTGGAGTGGGTCATCCGTTGGGATCTGTAGTGACCTCTCCTGAGGTTTCTTCCCAGCTGGTTCTGTCCTGCAGGACAGGGGACAGGTGTGTGCCATCTTAGAGGCTGGGACTTTTTATTCAGCAGGGCACACATCTCTCTAGGGCTGCAGAAAGCTGGGGAAGGGGGCAGAAGGTGTGTGTGTGTGTGGCCTGCAGTGGTGCTCAGAAACAGAAAACCTAGTGGGCAGCCTCTGGTTCTCCACAGAACTTGTGTTTCTGGCACTGGATGAAAGGACACAGGCAGAGGGTTTGGTTCTTGCTGGGGGTGGACTTGGGAACAGGCTGTGTGTTTGTCCCAGTGCTGGGTGCCTGCTTGGCTTCCCCCACCTCCACCCCCTTAGTCCTCTCCTCTGCGCCAGGAAAAGGGCAGGTGGACACATGCAGACACCTGTTAGAACAGGTGTCTGGACGGCCGTGGGAGTTCCTAGACCCTGGTCTTGGGTTCTGGGATCTTCCCTGTGAGGTTGAAACCTTCTCCAGTATCTCCCAGACTCCTCTCTGCGCTCTGGCCCTCCGTTTCTCCCTCCCCTACATCCAAATGTTAGGAAAATAGCTATGAACAGAGGGCGCTTTTGTCTGCGTCGGCCACAGGATCTGGACGGTCCCCTCCCCTGGGCTCTCCACCCCCCCCCCAAACCCCATGCTCTGACAGCCTGTTCCGTGTCCCCCCTTCCTCCAG
Seq C2 exon
CGCACAGTACAGAAAAGCGCCAAGTACATCTGCCTGGCAAACAAGGATTGCCCTGTGGACAAGAGGCGGCGGAACCGCTGCCAGTTCTGCCGCTTCCAGAAGTGCCTGGCTGTGGGCATGGTGAAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023034:ENSMUST00000023779:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.505 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(38.6=9.2)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGAGCTATTCCATGCCAGC
R:
CTTCCTTCACCATGCCCACAG
Band lengths:
344-1110
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