MmuINT0110542 @ mm9
Intron Retention
Gene
ENSMUSG00000023034 | Nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:MGI Symbol;Acc:MGI:1352454]
Coordinates
chr15:101103446-101105225:+
Coord C1 exon
chr15:101103446-101103624
Coord A exon
chr15:101103625-101104426
Coord C2 exon
chr15:101104427-101105225
Length
802 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CTCTACCTTCCCTGCTGCAGATC
3' ss Score
9.46
Exon sequences
Seq C1 exon
ATCTAAACCCGGTGAGGGGAAGCTCATCTTCTGCTCAGGCCTGGTACTACACCAGCTGCAGTGTGCCCGTGGCTTTGGTGATTGGATTGACAACATCCTGGCCTTCTCACGGTCCCTGCACAGCTTGGGTGTTGATGTTCCCGCCTTTGCCTGCCTGTCCGCTCTGGTCCTCATCACTG
Seq A exon
GTGAGTGGCAGAAACTAGACTGGGCCCAAGGGTTGCAGGACCATTGGGTAGGTAGCATCTAACACTTTGGGGACCCCTAGAGTGCCTGCAACATTGGGATGTTAGGACCTGCAAAGGGACTTAGCTCTATTCGCCCCTAAAGCTTAAATCAGCCTCCGAATGACCCCGGACTCCTCAGGTACGACTGTAGGCGCTGGGCATCTAGCTTAGGGATTCTGTTTGTTTAAAAACCTAGCTGTCAACCTCACAAGACACAGGAACGTGCACACATGAATTTTTCACATTCTGCGCTTGGATAGCTATCGCCATGGTCCAGAAACAGGACCTACTTCAGCTCTGTTGGGCTCCCTCCTTATTGTCTCTGTAAGAGGTAACCACTCTGCCAGCCTCAGTGGCATTCCTGTCATGGATTTTACTGTGCGTATCACAGGGTATGGACTCTAGTGTTAAATGTAGAGGTTTCTGGGTCCCTTCTGCTTCCGCTCCCATTTCCACTTAAATTTCTTAGGGGATCCTCCTGAGTAGATCAAGACCAGGAGCTGGATCTTGAAAGGGTAGGGAGTGATATCTACACCCAGCTCGTCCTTAGTCTGTCCTGCGAGACTCCAGGATTTTAGAACAGTGTGGAGCCTGGACCTCCAGAAAACCTGGATTAGGCTTTTGCCTTGGCCAGCCATTCAGTGGTTTCAAATATTGACCAGTCTGGACAGTGGGCTCCTGTGGGACGTGCTAGAGGGCTGGGGAAGCTTGTCAGGGAGAAGGCGTCAACTGAGCGGGGCTGACTCTACCTTCCCTGCTGCAG
Seq C2 exon
ATCGACACGGGCTCCAGGACCCTCGTCGGGTGGAAGAGCTGCAGAATCGCATTGCTAGCTGTCTGAAGGAGCACATGGCTACCGTGGCAGGAGACCCACAGCCGGCCAGCTGCCTGTCACGTCTGCTGGGCAAACTGCCTGAGCTTCGGACCCTGTGCACTCAAGGCCTGCAGCGCATCTTTTGCCTCAAGTTGGAGGACTTGGTACCCCCTCCACCTATTGTGGACAAGATCTTTATGGACACATTGTCTTTCTGACCCCTGCCCTGAACATGTGTGCGCACACGTGCGTGCTCTTCTGTCACCCATGTGCCTTTAAGCCTATAGCCCACGGACCCCCAGACCACCCTACCCCCAGCCTGGTTTTGAGCTAAGACTGACGTACCTCCTCACTCCAGAAGATGGACAGAGAACTCAAGACCTGGGGGAGGGTGTGTATTCACGGGGGTGACCCCACTATTTGTCTTATCCCTCCAGCTCAGTCCTGGCCTTCGTGTGTTTTTGTAAGATAAACCATTTTTAACACATACCACTCTGTTGTAAATAAGCTGACGCTACTGTAAATACAGAAAGGAAGAGGTTGAGATGGGGGTTGGGAGGAAGGGGTGGGGCTCCCACCAGCTGGGCGAGCCTCCAACTCGAGATCTCTTCCGCTCTCCTTCCATGTGTACATAACTGTCACTCAAGAAGGTGATTGACAGATTCTGATTTATATTTGTGTATTTTCCTGGATTTATAGGATGTGACTTTTCTGATTAATATATTTAATATATTGAATAAAAAATAGACATGTAGTTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023034-Nr4a1:NM_010444:6
Average complexity
IR-S
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(31.4=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(35.6=79.1)
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:
TCCGCTCTGGTCCTCATCAC
R:
GGTCCGTGGGCTATAGGCTTA
Band lengths:
358-1160
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: