Special

MmuINT0110551 @ mm9

Intron Retention

Gene
ENSMUSG00000028341 | Nr4a3
Description
nuclear receptor subfamily 4, group A, member 3 [Source:MGI Symbol;Acc:MGI:1352457]
Coordinates
chr4:48064120-48068931:+
Coord C1 exon
chr4:48064120-48065073
Coord A exon
chr4:48065074-48068801
Coord C2 exon
chr4:48068802-48068931
Length
3728 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TCTGTGTTATATTTTCTCAGAGA
3' ss Score
8.2
Exon sequences
Seq C1 exon
ATGCCCTGCGTGCAAGCCCAGTATAGCCCTTCACCTCCGGGGTCCACTTACGCCACGCAGACTTATGGCTCGGAATACACCACAGAAATCATGAACCCCGACTACACCAAGCTGACCATGGACCTCGGTAGCACGGGGATCATGGCCACCGCCACTACATCCCTGCCCAGCTTCAGTACCTTCATGGAGGGCTACCCCAGCAGCTGCGAACTCAAGCCCTCCTGCCTGTACCAAATGCCGCCTTCTGGGCCTCGGCCTTTGATCAAGATGGAAGAGGGTCGCGAGCATGGCTACCACCACCACCATCACCATCACCATCATCACCACCACCACCAGCAACAGCAGCCGTCCATTCCTCCTCCCTCCGGCCCCGAGGACGAGGTACTGCCCAGCACCTCCATGTACTTCAAGCAGTCTCCGCCTTCTACACCGACCACTCCAGGCTTCCCCCCGCAGGCGGGGGCGCTGTGGGACGACGAGCTGCCCTCTGCGCCTGGCTGCATCGCTCCGGGACCGCTGCTGGACCCGCAGATGAAGGCGGTACCCCCCATGGCCGCTGCTGCGCGCTTCCCGATCTTCTTCAAGCCCTCACCGCCACACCCTCCCGCGCCCAGTCCAGCCGGCGGCCACCACCTCGGCTATGACCCCACGGCCGCAGCTGCACTCAGTCTGCCCCTGGGAGCCGCGGCCGCAGCAGGCAGCCAAGCTGCTGCGCTCGAGGGCCACCCATACGGGCTCCCGCTGGCCAAGAGGACGGCCACGCTGACCTTCCCTCCGCTGGGCCTCACAGCCTCCCCCACCGCGTCCAGCCTGCTGGGAGAGAGCCCCAGCCTCCCATCGCCACCCAATAGGAGCTCATCATCTGGGGAAGGCACATGTGCCGTGTGCGGCGACAACGCTGCCTGCCAGCACTACGGAGTCCGCACCTGCGAGGGCTGCAAGGGCTTCTTCAAG
Seq A exon
GTGAGAGAGAGCATGCCTCCTCCAGGTACTTGCTCCGCTCAGCAGTCAGACCCCTTGCTGAGGCATCTAAGTGGGTGTAAGCTGGAGTCCTTGCCCTTGCCCGTGTGAAAGCTATAATCCCACACACCGTGCATTCCTAGGCCTAGAACTTCAGACCCATCTTTCCCAGGGTTTTTAAACTCAAAAGTTCCCGAATAAGCTGTCCATGCACTTGAAGGGCCTGCATCAACCTCCTGACCTGACATTTCCTTAGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTTGTTGTTTCTGAACAGAGGTTTCTGCAGATTTTTAAAAGGATCCAAACTCCCACACCACCCAAACATCATCATCCCTTCTCTGTCCACCCAGAGTGTGAGAAAATAGCACCCTCATGCATGGCGGGCCTGGGCGTTAGTGTCTCGGTCTTCACAGGAAGAGCTGCGAGACTTAAGATTGAATGTTGGTCATTCACGGGCTGTTTCTGATTCAGTGTGCTTGGAAACTAGATCTTAATTATCGTTGTTTCTTAGAGGAGAAAATGGAGGTTCAGAGAGGTCATTCAATTGCCCCAGAACTCACACTCAGAGAGTGAGGTGGAGACAGGGGGTCAACTCATAATCTGTGTGCTCCCAAGATGCTCTGTGGTGGCAGAACCGAGGGGCAAGGTAGCTGGCTCGAGGCAGCTTGGGACAGCTTAGTCCATGGAAGGGTAGAAGGTAGAACTCAGGCCTTGCCAATCTACCCTGTCCTCTAGGAACGCTTACCTCCCTGCATCTGTGCACACACAGTGCCCACGACCATCATTCTCTCATAGACACAGTGGAGAATTGGAGAATCATCGGCCTCCCCCATATTAGCAAAGAAACTGAACCCTGGAGAAGTATCCTATACTCAGGCTTGTGGAGCGATGTGGCTTGCATATGGGATAAGGGACAGCTGGCTTCTCTTGACTCTGGAGTTCAATAGTCTTCCCCCCACCCCTGCCCCACTATGTGTGTGGGGGGGTGCAGTGGGGAGGGGGGGTTCAGCCTTCTTACTCTTTTGCTGTTCTTTCCGTTGTCACTGAGTCTCAGATGGTTCCAGATATTTCTGTGTCATTCTCTTTACACCCTAACCAACTGATACTTCAGGCACAAACAGACTCACATGAATAACATAGATGAAGGGGGATACTGATTGGGTGACAAGGATTTGGGAAGCAGAAAGAATGTTTATTTATGAGCCGGAATCGGGGCTGGAAGATTCAAATAGGAATCCTAACTTGACACCTATCCATTTGTAACATTGGACATAGGCCTTCTTTCTAGATCTTAGCTCCCCAACCAGCAGATCAAACACAATGAAAAGGCCATAGTAAGTAAGATATCAACATACAAGAGCGCGCCCTAGTCTTTAAGTCACAAAACAATAGGTATGGAATGAAGACTTGGTATTTATGACCATGCACACATTTGTGGTTAGATATACAAACCGACAGGCATCCGGTTGTCACATGACAATGGCTATCACATCACTCACTGAATTCTCCAGGTAAATGGAAGGGTGCTTGGGTAAATATGTTGCCATGTGCAAGGCCCCACAGATACACAAGTTTGTGATGCTTTAAGGGCGCACCTTCCTTTTAAATAAGCCGCTTAGGTTGCCTTTGTGTTTTCCCTTCAGTGTTAGGGGCTGAATCCGGGCAGGTGCTTTACCTCTGAGCTGGTCTCCAAGCCTGGGTTAGCCTCCCCCTTTTCTTCCTTTCTCCCCCTCCCCCTGCTACTCTGGGGGGGGGGTCCCATATAACTACATTCCTTTAGCGGGTTTGGATTTTATAAAATTTCAGTGGAAATGCTGAAGGGTGATAAACAGTCAGCAGGAAGGGAGAAAAGAAAGACATTCCAGGAAGAGATGAATGAAGACTACACGGCAGAGCCATCCCCAAACATTGAGAACTTAGTACCCCCATGGGAGTGTTAACATCTAGAAACTCACAGCAACCTTTCTCCAACACTTCCCTTTTCTTCAGCATTCCCTTGAAAACAGATCTATATTGGAAGGAAGGGTGGGGGCAGGCCAGGGTTAGGACCACCCCACAGATCTGTTAATTAAAGGAACTAGAACTGGATTTACCCAGTGGCTTTCTACCATTAAATTGAATTCTTTAAAAATGTGACATGAAGTGCAGTTAATGATGGGAATTCGGAGATTGAACTGTAACGATCTCTCGGTCCTTACACTGTGCAGACACACACAAGTGTGGAGGCCGGCTTCGGACTATTGGGGAAATGTACACCTGCAGCAGAATGCCACAGGCGCTTACATCCATCGGCACAGTGCCTTGGGGATAATGGCAGGAAAGGATGCTAGAAAGCATGGGCATGTTCTCTGAAAGAGAGCTTCATTCAAAGGCTGCTATCAGTGTAGACTGCTGAGAATGGAGGTGCTGAAAACTCAGCCCTGTGCAGCTGTGCCTTAGACTTGACATAGGCTGGCCTTGTCATATGTATAACCGTTCATTCCCTTAGGTGAAATGAACACATGACAGGGTAAAACTGAATCCTTGGGAAATAAGGAGAGTAGAGAATAAAAGCCGAAAGTAAAACTAGAATTTTTGAACCCAAAACACATCACCAAGCACAGCTTATCTAAACTTCTTTTAAAACATAGCCCAGACTTCCCAAATACATTCCAGTGTTCTGCTCTGAGTGGAATCCTGTAGATTCTGGTCCTTTTGGAACACTTCATTCTACGTGAAAAAATGTAACCATTTGCACAAAGGTTTTTTATGACTTTTTAAGCATTATTTTACATGTGGAGCATAGGAGATGTTTAATTATTGCCCCATGTGTTATTTCAAAATTCTATGTGATTCAGAAATATGTGATGTTATTTTTATCTCCAGCATCAAGTTTTATGGTGTGCCTTTAATAATGTGGTTCTTTTTGGTGTCTGAAATAATAGTCATTTATGAAATCCTGAGGTGTATATATGGCTTTCCTATTTTTTTCCTTCTCTTATTCCTACTTGGCTTTGGGTTTTCATTCCTGGATATGACAGTGATTTTTCTACCCAACTTTAAGAATGTGCTTTTCAAAGTCAGAAATGGACAGTTTATTATATGCATCCTCTAAAGATAAAACAAACTAAGTAGTACAATCACATGGATTTATTTTTTTTTAGTTAAAACATGATTTCTTATATGTTTTAGAATGAAAACATTATTTCCTATACATTTTAACAAGACAAACTCAGATTTTATTCTGTATGGCTTCACCTCTATTGAGTAACAAAACCAGTTATTGAGATGTCTGGCAATGTCTGGTATAATAGTGATACCATACATAGTACAGCCCAGATAGTTCTGATTTTATTTTAATAAGGTCAGTGATAATCAGGGGAGTAGAACAAGTAGAAAATTGTTCCCAAGGGGATATTAAAAGTGGAGATAATCTAATCCTCCAAGGTACGATATGTTGACCTGGTAATTTCAGATATGATTTTATCATTCAGAGTTGGGTGCCTCCTGAGACTCGCTTCAGAACAACCCAAGATGATTTTCACTGTCAGCCAGGAACACTAATAAAATTGTTTTTCCTGCAGGCTAGCGTGTTAGGAAATTAAATTTATCTAATTATACAAATTGCACTGTCGCTTTTCACGTTGTAATTAAAATACATCTTGTCAGGTCTTGCCTCTTTCCAGAAACTATTAGTTGACTATCTCTGTGTTATATTTTCTCAG
Seq C2 exon
AGAACGGTGCAGAAAAATGCAAAATATGTTTGCCTGGCAAATAAAAACTGCCCAGTGGACAAGAGACGCCGAAACCGATGTCAGTACTGCAGATTTCAGAAGTGTCTCAGTGTCGGGATGGTTAAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028341-Nr4a3:NM_015743:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.564 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0253517=Zip=WD(100=34.9),PF0010513=zf-C4=PU(38.6=8.5)

							
A:
NA

							
C2:
PF0010513=zf-C4=PD(58.6=93.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000121455





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000030025
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:99828994-99832688 
ALTERNATIVE
HsaINT0115663
(NR4A3)
Human
(hg19)
chr9:102591276-102594970 
ALTERNATIVE
HsaINT0115663
(NR4A3)
Rat
(rn6)
chr5:63788781-63792506 
ALTERNATIVE
RnoINT0103000
(Nr4a3)
Cow
(bosTau6)
chr8:65342186-65345799 
ALTERNATIVE
BtaINT0103606
(NR4A3)
Chicken
(galGal4)
chr2:89390716-89392578 
ALTERNATIVE
GgaINT0099331
(NR4A3)
Chicken
(galGal3)
chr2:91705588-91707450 
ALTERNATIVE
GgaINT0099331
(E1BYS2_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
Functional annotations
(Submit an annotation)

	


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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"