Special

MmuINT0113508 @ mm9

Intron Retention

Gene
ENSMUSG00000026761 | Orc4
Description
origin recognition complex, subunit 4 [Source:MGI Symbol;Acc:MGI:1347043]
Coordinates
chr2:48789070-48792382:-
Coord C1 exon
chr2:48792292-48792382
Coord A exon
chr2:48789143-48792291
Coord C2 exon
chr2:48789070-48789142
Length
3149 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAAA
5' ss Score
-1.7
3' ss Seq
TTACACATTTTTATATTTAGTTA
3' ss Score
6.18
Exon sequences
Seq C1 exon
GCATTTGATTGAGCTACTCAAAAGAACTGCTATCTATGGAGAAAGCAATTCTGTACTCATTGTTGGACCACGAGGATCAGGAAAGACCACA
Seq A exon
GTAAAAGACTTAAGTTTCTCATATATCATTGCTTTAATACACATTTGAAGTTTTTATATCAGATACACTAAAAATGTTTTTCGTTTTATTGTCTTGCAACATTCTTTGTTTTCTATTCCTTTTAAATGACAAAATCCATGCAGGTATTCTACAAAGTTAGGTTGTGGTATGGGAGTTGATCATGCTTTTTATGTTCTCTGCTTGGTATATTGCCCTATACTGGGGCAGGGATTTCAATCCTCCCATCTGCCACTGAGAGTATAAGGTCCATGCTTCCATACATACATGGGCTCTGAGGGTCCCAACTCAGGACTTCACGGGTCATCATCATACAGTGATTCCCCACAAGCATTTTTACCCCTTTTTACAGTTTTCACAGTTTTACAATTTATTTTTAACCTTCAAACAAATCTTTCATGTCAAGGTCATCAGTATTTATGTCATATTTCTCTTCTTCTGACTTAGTTAATCTCAAAAATTCTTCTCCCTCTCATCTGTTCCTTTTTACAATATACAAAACAAATACATCAACATTTGAATGTATTACTATTAAATTTTAATGTGCTAAGTTGTATAAATTGTATTTTTCTAGTATTCTGTAATAGCAAATTAATATTTTGTTCAGGCATATTATTATACCTTAAAAATAGTTAAGATAGTAAATTAAAACTGTTTCTATTTTTTAAAATAGTACATGTTGGTTCTATATTATGTAAGATGAAGAATTTTTATTTATACTACCATTTCCATTTAAAGAACATAACTTGGTAATTGACAACTTTATTACTGTTTCAAGAATTTATACATTTCTTATAAGATGTCTTACTCTAGCCTGCTTTGGTCCTCCTGCTTACTTGGTATAATTTCCAATTCTTTGCCATTTGTTGTTGTTTGGTTTTTATAATTTTCTTTTGCTTTAATTTAACAACTTTTTTCAACAGAAGAACTATGTAAAATACATTTGTGGTTTTGATTGTTTTCCTTAATGTATCTACTGCCTGGGGTTATAGGCTTCCTCACAGGTGTTTTTGTTTTTGTTTTTGTTTTTCCTCTCCTTAGAATTGCAAGGATTTTGCATGAATTTTGTTTTGTGGAGAAAATCCTGGAGTGAGATTTTCTTTAGTTTTTCTTTTTTCTTTTCTTTTTGCTGTATTTAGATTATATAAGTGGCTGAGCCTCACAGAAGTCTCAGATCCCTGTGGCTTAGTAGGACATTTTATCTTTCTTTGTACCGTCTATCATAACAGTGTACAAATCAAAGGAAGCAAGCTTGTGTAGATGAGCTCAGTGGAAGAGTGCTCAGACTCTCTTGATACACTTAGGAGATAAAAAGTTTTACTAATGTCTATCCTTTAAAGGATTTGAAATGTTTTCTAATGTGTGATTCATGAATTGAAACAAAATGGCTCCCAAGTAAAATATAAATGTCAGTGAAATGTAAGAGATAGGAGGCAGCACACAATGCAATACTTTTTAAAAATACGTTGAAAGTAGTGTTGTTAGGGAGAAAGTTTGTATGAGTCACAGATGTTCTCTTGTGATAGAGTCGATCTGATTGAAAGATAGGAAAGTACTGTCTTATCTCTTATGGTTGCTTTTATTGTTTCTTCTCAGCTGAACTACTACAGAAGTCAGACAGTTGTACCCAGAGAGGTTTTTTTGTTTTTTTTTGTTTGTTTGTTTGTTTGTTTGTTTTTTTAAGAGAATCTAGATCAAGAGTACCTGTGTATAATTCCATGTGCTTAAAATCCACACATACCAAAGTTAATTTCTATGTTTACTATCCTTTTGTAAAATCTGTCTACTCTCTTTACTTATATGTACACCTAACCTCTGTTTTCCTGGACCACTTTTTTTTTTTAAATTTTATATCTTTTTTCCCCACATTTTTTATTAGATATTTTCTTCATTTACATTTCAAATGCTATCCCAAAAGTCCCCTATACCCTCCCCAAGCCCTACTCCCCTATCCACTCACTCCTACTTCTTGGCCCTGGTGCTCCCCTGTCCTGGGGCATATAAAGTTTGCAAGACCAAGGGGCCTCTTTTCTCAATGATGGCCGACTAGGCCATCTTCTGCTACATATGCAGCTAGAGACACTCACTCTGGGGGTACTGGTTAGTTCGTATTGTTGTTCCACCTATAGGGTTGCAGACCCCTTCAGCTCCTTGGGTACTTTCTCTAGCTCCTCCATTGGGGGCCCTGTGTTCTATCCATTAGATGACTGTGAGCATCCACTTCTGTATTTGCCAGGCACTGGCAAAGCCTCACAGGAGACAGCTATATCAGGGTCCCTTCAGCAAAATCTTGCTGGCATATGCAATAGTGTCTCCTGGACCATTTTTGATGTGAATAAAAGTGTTTTACATTGCCCTTAATCTTCTTCATTTACAAATTTTATATTACAATAATACATTCTCAGTATAAGTACATTTTCATAGTAATTATTATTGGTAATCTTACAATTTCATCTAACCTTTTACTAACTTTTGTATTGTTTTTTGTTTTGTTTTGTTTTTTGTTTTGTTTTGATTATTTGTTTGTGAAACAATTTCATATAGTTCAGGTTGCAGGTCATCCTGACTCTTCAATTTCTCACTCTTTGCCTTCACCTCCTGAGTGCTGGGATTACAGGCTAATTGCTGCTGCGTCCAGCTAAATTTCATCACTATGCTTTTCTATTCTTGTTCATGAGTAAATAGTTTATATTTTTCTTTTTAACTATTTGCTATTTCTTATTTCATGACAATATGCAGACTATCAACAGTGTTGCATAAAATTGACATTGGAGGACAAACCTTTTACAACTATTTAGGTTTATTTTTTTCTATAGCTTTTAACTGCTTTCAGTGGCACCTGGTAGAGAAATGTTACTGAATAGTAAAATGTACTGAGTCATAGAGATTACAAAAGAAGGTTTTATGATTGCTTCCAATGTTTATTAATAGTTTATATAAATTATTAAGATATTAAAGTTTCAGTTAGGCTTTGCCATTAGACTTAGACATAATGAATTGTATATATCTAAACCTATTAGCTATAAAGTAATTTATTTGTTTATATTTATTCTCAACATTTATGATTTTAAGAAAGAATAGCTTCATTTTATCTTTTCCAAATTAAACATTTTACACATTTTTATATTTAG
Seq C2 exon
TTATTAAATCATGCTTTGAAAGAACTCATGGAAATAGAAGTGAGTGAAAATGTGATACAAGTTCACTTAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026761-Orc4:NM_011958:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.002 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF131911=AAA_16=FE(19.5=100)

							
A:
NA

							
C2:
PF131911=AAA_16=FE(15.6=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028098





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028098f1985A, ENSMUSP00000088497, ENSMUSP00000117732, ENSMUSP00000119274, ENSMUSP00000121114
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:147958867-147972738 
ALTERNATIVE
HsaINT0118476
(ORC4)
Human
(hg19)
chr2:148716436-148730307 
LOW PSI
HsaINT0118476
Rat
(rn6)
chr3:33058994-33061809 
LOW PSI
RnoINT0105623
(Orc4)
Cow
(bosTau6)
chr2:48335022-48344396 
ALTERNATIVE
BtaINT0105841
(ORC4)
Chicken
(galGal4)
chr7:34068751-34069881 
ALTERNATIVE
GgaINT0046406
(ORC4)
Chicken
(galGal3)
chr7:36196354-36197484 
LOW PSI
GgaINT0046406
(ORC4)
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"