MmuINT0110540 @ mm10
Intron Retention
Gene
ENSMUSG00000023034 | Nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:MGI Symbol;Acc:MGI:1352454]
Coordinates
chr15:101272153-101272920:+
Coord C1 exon
chr15:101272153-101272304
Coord A exon
chr15:101272305-101272717
Coord C2 exon
chr15:101272718-101272920
Length
413 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CTTACCTGCGTTCCTTTCAGTTC
3' ss Score
10.9
Exon sequences
Seq C1 exon
TTGTACGGACAGACAGCCTAAAAGGGCGGCGGGGCCGGCTACCTTCAAAACCCAAGCAGCCTCCAGATGCCTCCCCTACCAATCTTCTCACTTCCCTCATCCGGGCACACTTGGACTCCGGGCCTAGCACTGCCAAATTGGACTATTCCAAG
Seq A exon
GTGAGGTCTTGCCCGCCCATCTGCCCTGCCCTGAGAACATATGCAATGCCTTTGTGCCTGTTAGGAAAGGCTCTCCCTCCAGGGCAACATCAGGAAACAAGCATCCTCTATGTACTGGCTAGTTGGAGAAATGCATTGGGATGGGTGTGGGGTCGGGGAGCCAGTTACAAACAGCTGCCGTAGCCCTGTTTTCCTGTGGGAATTGACAAGCACATGGGCCCAGAATAGGGCTCTTTTGCACGCCTGGATCTGGTGTCCCAGTGCATGAGAGCTCTGTAATGCAGCTTGTGTAGGCTTTGCTGTGGACCCAATGCAGGACACAGCTGTGTGATGCAGGCCTTGCTGTGGAGCCAGTGCGTGACACAGCTGTGTGGTGCAGGCCCTCATGTGGAACTTACCTGCGTTCCTTTCAG
Seq C2 exon
TTCCAGGAACTGGTGCTGCCCCGCTTCGGGAAGGAAGATGCCGGTGACGTGCAACAATTTTATGACTTGCTCTCTGGTTCCCTGGACGTTATCCGAAAGTGGGCAGAAAAAATCCCTGGCTTCATTGAGCTTTGCCCAGGAGACCAAGACCTGTTGCTAGAGTCTGCCTTCCTGGAACTCTTCATCCTCCGCCTGGCATACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023034:ENSMUST00000023779:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.353 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0010425=Hormone_recep=PU(32.5=91.2)
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:
CGGACAGACAGCCTAAAAGGG
R:
CAGGCGGAGGATGAAGAGTTC
Band lengths:
342-755
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