Special

MmuINT0041254 @ mm9

Intron Retention

Gene
ENSMUSG00000045438 | Cox19
Description
COX19 cytochrome c oxidase assembly homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1915283]
Coordinates
chr5:139818517-139821120:-
Coord C1 exon
chr5:139821026-139821120
Coord A exon
chr5:139818629-139821025
Coord C2 exon
chr5:139818517-139818628
Length
2397 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGG
5' ss Score
8.99
3' ss Seq
TGGCTTTCTTCTTTCCCTAGGTG
3' ss Score
12.44
Exon sequences
Seq C1 exon
GGATTTCGCCGTGATGTCGACCGCAATGAACTTCGGGACCAAAAGCTTCCAGCCGCGGCCCCCAGACAAAGGCAGCTTCCCGCTGGACCACTTCG
Seq A exon
GTGAGGCGAGGCGAGGCACAGGCTGATGGCGGCCTGGGATCGGGTGGCAGAGTTAGGAATACTGAATCTGGGTGGCAGCGTCTCGGGTGCTGAGTCTGAGTGGTAGGGAGTGCTGTTTCTCGGTGACAGGATCAGGGGTATTGGAAGTAGGTGGCAGGATCTGGGATACTGGTTCTAGATGGCAGGGTCAGGGGTACTGGGGTACTGGGTTTGGGTGACAGAGTTATGGGTGCAGGATATCTGGGTGGCAGGGTCAGGGGTACTGGATCTGGGTTCAGGGTCTGGGCTGCTGGGTCTGGGTGGCAGAGACTGGAGTGTTGTCTCTTTGCTATAGATGGCAGGTTTGGGGGCACTGGGTTTGGATGGCAGGGCCTGGGGTTGTAGATCTGGGTGGCAGAGCCTAAGGTACTAGATTTGAGTGGCCGGGTCAGAGTTGCTGGATTTAGGTGTAATGTCTGAAGAGTTAGATGTTGGATGTGACAGGGCCTAGGGTGCTGGATCGAAGGTCTGAGAGCCAAAGTGAAGGAGCTGAATATGAGGGACAGTGTGTGGGGTTATAGACCTGGGTGGCATTGTCATGTGTGTTGATGACAGGATGCTAGAAATGGTGGGTGGGGTCTGAGGTACTGGACCCTGGATGCAGAGCAGTTAATATTACAGGTCCTTCCCGGGTAGTGGGGCTGGGCGTGCTCAGAGCACTGTGGGGGTGCAGTCAGAGAAACTGAGTCTTGAGGGCCCCTATTTCAGAGGGCCACATGTCATGGCTCTCCAAGTAAGACTTGGGGCTAATGTGATAGGATGGTGACAGGCCTCCTGGAACGGAGCTTGATGTTAGGCCCCCTGGCGGCAGCTCAGCTCAGCGCAGGACATACCCACCCTCCCCTAGCTCCAGGCTCTGGGTCTGCCGTGAACATTAGGCAAGGAAATATTTTCAAAAAGCTTTTTGATATCTAACACTGGGGCTGAAAGCCCGGGTTTGGCACATGCTAGGCGAGTGTTCACCTCTGAGCCACGCCTCCAGCCTGGAGGATTTCTAGTCACCGTTCTGAAGTCTGCAGTTAACAGGCCTTTTGGGAAACTGGAACATGGGAAAGAAAAAAAACAAACAAACTGGGAGAGAGTTGGAGATTCAGATTACAGAGGCCGAGCTGGTGCCTGGCACGCACAGGAACCTGAGTCCAGTCCTCAGCACTACAATAATTAAAAAAAGAAAAGACTGCCCTGCCTACCACCAGCACATAGGACATCCCCCCCCCCCCCACCTACCACCAGCACACAGACCTCCCCACAAGTCCTACCACCAGCACACAGCCCTGAGAGATGCAGCAGCCCTCAGCCCTCGTGTTAGTGTAGAAACGGCAGCTGTTAGTGTAGATTAGACGCTTCGGTGAACTGCTGTAGAGACTCCAGCTCCAGGGACAGCTTTAGAGATTACTGGTTTTTTGGGTTTTTTTTTTGGGGGGGGGGGTTCCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGTCCTCGAACTCAGAAATCCGCCTGCCTCTGTATTTTTTAAGTTATGCTTATTTATTTAGTGTGTTTGGGGATATGCCATGACACGTATATAGTCAGAGGACAAACTGTGGAAAACTGGGATCTCTCCACCCCCACGTGTGTCCCAGAGATCAAACTTAGGTTGTCAGCCTTGGTGGCAAGCGTGTTTACCCACTGAGCCATCTCACTATTTTTAGATTATGATTTCATTGCCAACATTTCATTGGGAAATTTTCCATTTAAAATTTTTATTTCAATTCGTTATTGATTCTTCATTTTTTTTTCAAAGGCAGGGTCTCACTATGTAGTCCTGGCTGTCCTGGAACTCGCTGCGTAGACCAGGCTGGACTCAAATGTACAAAGATCCACCGGCCTCTGCCTCCTGAATGCTAGAATTAAAGGTGTGTGCCAATATGACCGGCTTTATTATAATTTTTTTAAGTTTATGTGTATGTGTGTGCATCTGAGTTTGTATATACACCATTTGTATGCAGGCACCCTTGGTGGCCAGAAGCAGGTTTTTGATAGCCTGGAGCTGAAGTTACAGGCATTTGTTAGCTGCTCAATGTGTGTATCAGGAACCAAACTCAGGTCTCTGTCAGAGCAGCCAGTGTTCATAGCCAGTAAGCCATCTCCCCAGCTTCTTTCAGCCCTTTTGTTTTGAAGTACAGGGATTTGAACCCAGGGGACTATATGCCAAACATACACATTACCTCAGAGCCACACCCACAGCCTCACAAAGGGAACGAATTTTGATGGAAACCCTAGTGCTGCTCCTAAAGTCAGCGTGTGAGCGGGTCAGGCCTTCTCTTTAACTAATAGAATGCTGGCTTTCTTCTTTCCCTAG
Seq C2 exon
GTGAATGTAAAAGCTTTAAAGAAAAATTCATGAGGTGTCTCCGTGACAAGAACTATGAAAATGCTTTGTGCAGAAATGAATCTAAAGAGTATTTAATGTGCAGGATGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045438-Cox19:NM_197980:1
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=0.473 A=NA C2=0.026
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF067478=CHCH=WD(100=92.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000062046





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000062046f5933A, ENSMUSP00000062046f5934A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:973293-975427 
ALTERNATIVE
HsaINT0040372
(COX19)
Human
(hg19)
chr7:1012929-1015063 
LOW PSI
HsaINT0040372
(COX19)
Rat
(rn6)
chr12:17395734-17398243 
ALTERNATIVE
RnoINT0041063
(Cox19)
Cow
(bosTau6)
chr25:42316476-42317045 
ALTERNATIVE
BtaINT0042980
(COX19)
Chicken
(galGal4)
chr14:2235796-2235895 
ALTERNATIVE
GgaINT0014558
(COX19)
Chicken
(galGal3)
chr14:2242409-2242508 
ALTERNATIVE
GgaINT0014558
(COX19)
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"