Special

MmuINT0118759 @ mm9

Intron Retention

Gene
ENSMUSG00000026873 | Phf19
Description
PHD finger protein 19 [Source:MGI Symbol;Acc:MGI:1921266]
Coordinates
chr2:34749275-34752672:-
Coord C1 exon
chr2:34752577-34752672
Coord A exon
chr2:34751582-34752576
Coord C2 exon
chr2:34749275-34751581
Length
995 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTCTTCCCCTCCTGATACAGATG
3' ss Score
9.44
Exon sequences
Seq C1 exon
TGGCAGCTCAGGCCAGACCTTCTTCTCAGATGTGGATTCTACCGACGCAGCCAGCACCTCGGGGTCTGCCTCCACCAGCCTCTCCTACGACTCCAG
Seq A exon
GTGAGCTTCCTGAGGGTGTGTGCTGCAGCCTTGCACAGGACCGTGGTCTGCAGCCTGGCCACTCCCTACTGCTGGCTGCAACCTTTTGGGATTCTTTGCCTGCAGTGGCTATGTGATCCCTCTAGTCAAGTGACCCAATTCTGGGACCGTTTGATTAAAGAATCCATTTCCTTCTGGGCTTCTTGGCATCTGTGGGTCGTAACTGTGCCATCTGTGCCTCAGACTCCTGTTCTCCGTTCCTGGCTGTCTGGTTTGTATTCTAGGATCATTAAGAGGAAAATTCATTTCTTTTAAGCAGAGTAGAAAGGTAGAGTGTGAGGTCTGGCTGAGAGTATAACCTGGTTTACTGCTGGCCACAGCCCCCTCTGCATTCGTATTCTAGAGTATTTGGAGACTTTGTGGGTATAGATAGAACTTGTCTGCTTGTGCACCTCTCTGCCTGGGCTCCTTCTCTGCTGTTGCCTCTGTAGCTTTAGGAACCAAGCCCAGGGCTTCGTGCTTACTAGACAAGTGTTCTATCACTGAGCGACACGTCCCTAGTCTTCCTGCCCCCTTGAGTTCTCACTACACCTCCATGTCTCGGCATCTGTTAACAGGCGGTTTGTCTAATGTGTCTGTTTTGCTAGCTCCTCTGCCTGCGTGGCGCAAAGCCCTTCAGTTTCTGTCCCTACGTAGCTCACCCAGCTCATACAAAGGACTGAAGAGCCTAAGCAAGGTCTGCACTGCGGGACTTCAGAAGCACACACCGCAGTGACCCACCCTTCCAGATACAAACAGCATACGCTTTAAAACTGAACATACCCAGCTTGAAATCCTGGCCTTTGTACTCCCCAACCAATGTCCTCTCTGGAGCCTCAGTTTCCCTAGAACAGGACTACTCTGAAGTTCCAACAAGACAATCCATGCCCAGGGTCCGGCCTAGTCCCTGGTACCTAAAGGCCTCTCGGGTTGTTTCCACTCATCCCTAGCATCTCCCTCTTCCCCTCCTGATACAG
Seq C2 exon
ATGGACGGTAGGCAGCCGCAAGAGGAAGCTGACAGCCAAAGTGCACAGGCCCCTGCGAGCAAAGCAAAGGGCGGCGGAGCTGGAGGGGCGCTGCGCCTCAGACAGCAATGCAGAGGGAGCTGTGGGTCCTGAGCAGCCGGATGAAGGCATCGACAGCCACACACTTGAAAGCATCAGTGGAGACGACTCGTCCCTGTCCCACCTCAAGTCCTCTATCACCAACTACTTTGGTGCAGCTGGGCGGTTGGCCTGCGGGGAAAAATATCGGGTGTTGGCGCGGAGGGTCACTCCAGAAGGCAAGGTTCAGTACCTGTTGGAATGGGAGGGGACCACCCCTTACTGATTACCCTCAGAGGCTGCCCAGATCCCTGCAAACCAAAGGAGGGGCAGAAGAGGCCACTGGGTCCCTGTTTTCGCCAGGCTTGGGGTGGTGGTGGTGAAACAGGACATCCTGCCTGTGGCCCCTGCCTGCTGCCTGCCAGGCCAAGGCCTGTGTGCTGCTGTACCTGAGTCTCTGAGACCCCATTGGTATTCTCTCGTTGTCAATACTACACTCCACACCCCTCAAACTTTTTATTGGTTCCTCTGACAGTATCCTGGCTCCAACCCCTGGATCTGTTTTTTGTTGTCCCCAATTCTCCATCTTCTGCCCTCTCACCCCTTTCAGGTGTTTTGTGTGGACACACATCTTCCACGGGCATACACCCATCTGTCCCTCACTGGGCATGCTTCACTGGGTCCTCACTAGGACCACAGTGAGGGAAGGGAACCTTGGGGGTCTTCTGCTTTCTCACTAGTACCCCTCACCCCAGGAAGGTAGGGGGTGCCTGAGAAAGTTTAGGATGCCTAGGACCCAGAGTCTGGGGAGTGGTGAGCTGGGTCTCTGCAGAAGGGACAAGAATCAGGGTCTTTTATTGAGGAGGGGAGACTAAGGAAGTCAGGCAGGGCCAAGGTTTCCAGAAGTTTGCCTGTCCCAGCAACAACCCTTTACTGTTGTCAAGGATTGGGACCTGGCCCTGCTGCATAGACGTGTCTTAAACACACAGATCTGGGAGGAAAGGATGGGGAAGAAGACTAAGCCAGATTAAATCCCATCCCAAACACTGTGTGTACAGCCACCACCTACTCCTGCCAGGGCCCCCTGGCCCCCCGTCCTTGGCCTCTTCCAGGGATACATGCTGCAGTTAAATGTGAGAACCAAACCCCTGCCTCCTCTGGCCTGTGAAGCAGCCTTGGCCCCACAGAGAAGCACAAAATATACCCCTCTCCTGCATGGCTCCTGCCTTGCCCTGGAGCTGACAATCACTTTGGGGACAGGTTTGGAGTTTACAAGGGCCTGAATCGTTGGTTCCCTTCAGAAAGGAAGGCTTTGTCATCAATGGTACAAATAGAATTCTTAGAATGGTCAAGCTTAGCCGTGTCTGGGGAGAAACCAGGAGGTGGGCAGGGAGCCCTTACTTTGCCTACAGAAACAGAAATTGACTCACTCAGTTGGAGAAATGGAAAGAACTGCCATTGAAGTGGGAGGCAAGGGCACCAGACTGAGACTAGCCTCCCTGACTGCTGCTGTAGCTTCCAGCTGGGGGTGGGAAGATGGACCACATGGTGACATCAGACTATACCAAAGGTGCTGATATTCCCATGACTAGGTCTGACCCCTTCACACCTTCCCGTGAGCATTAAGGAGGGTCCCTGCAGTAGGTTAGATGTCCCCTGCCTTAAACCTCAGCCACCATGGTGCCTTGCAAAGAAACCTCGCCTCTCATAGACACAGCTACCTACTTCCCTCTGCCTTCCTGTCTGGGCTCAGGCAGGGATAAGCAGATGGACACTGGGCCCAGTTGTCAGTCCCACAGCTGCCGCCACTGAGGTCCCAAAGTGGGGCCTGGTGGAAGGAGAGTTGGGAAGCCAACTCCTAGGCTTGTGGGAACTGGGGTCAAATTTGTGGCTTCCTGTTGGCTTCAGTGAACATGGCAACCTCCAACACGTGTTTTCCAGGCCACTGGGGAAGCCAGAGTTAGGATGGCTATCTGTACATCTGCCCCTCCTCTGCTGTGCCCCAGAAGCTCTGGGCCTGAGGAGCAGGAAGGCAGGAGGGGTGCCCGTCCCGTTGGGGATCCTAGCACAAGGCCTGACCAGGTCCCTGGACTTCCCATGGCAGCATTTCACTCCTACAAAATAATAGCTGCATTACTGCCAACTGATGGTATAACCCTGTGCACCTTTGAAAAGATTTTGGTTTTAAATTGCTGCTTTTAATAATATTTGTTATATTAAAGTTATAATTGATGTGTCTGGTTTACAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026873-Phf19:NM_028716:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.394 A=NA C2=0.360
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF140611=Mtf2_C=WD(100=44.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028232





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr9:120858287-120860089 
ALTERNATIVE
HsaINT0123949
(PHF19)
Human
(hg19)
chr9:123620565-123622367 
LOW PSI
HsaINT0123949
(PHF19)
Rat
(rn6)
chr3:13959480-13960616 
LOW PSI
RnoINT0110355
(Phf19)
Cow
(bosTau6)
chr8:112143964-112144948 
LOW PSI
BtaINT0110736
(PHF19)
Chicken
(galGal4)
chr17:8288994-8289079 
ALTERNATIVE
GgaINT1021403
(PHF19)
Chicken
(galGal3)
chr8:14690701-14692802 
ALTERNATIVE
GgaINT0037231
(MTF2)
Zebrafish
(danRer10)
chr8:12304808-12322546 
LOW PSI
DreINT0113287
(phf19)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CAGCCTCTCCTACGACTCCAG

				
R: 
CCCCTCCCATTCCAACAGGTA

				
Band lengths: 
349-1344

			

		

	





	
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"