Special

MmuINT0118746 @ mm9

Intron Retention

Gene
ENSMUSG00000025764 | Phf17
Description
PHD finger protein 17 [Source:MGI Symbol;Acc:MGI:1925835]
Coordinates
chr3:41392856-41395762:+
Coord C1 exon
chr3:41392856-41392944
Coord A exon
chr3:41392945-41395604
Coord C2 exon
chr3:41395605-41395762
Length
2660 bp
Sequences
Splice sites
5' ss Seq
GAGGTACTT
5' ss Score
7.82
3' ss Seq
TCCCTTTCTCGTCTCCCCAGGTG
3' ss Score
13.71
Exon sequences
Seq C1 exon
GCTTGTCAACGACATGGTCCCAGCATTCTCGATCCCAGCATGGGAGGAGTAGTACCTGCTCTAGACCTGAAGATCGAAAGCCTTCTGAG
Seq A exon
GTACTTCTGAATGCTTGCTTGCCTTGATCATGTGTGCTGTAAGTAAGTGCATGCGAACCTGCCGCCCACATGCCTGCCCCATGCTGTGCAGGTCTGGGCAAGTGCCCCACTTTATACCCCGGCAAGATGGTGAGAAGCAGATGTGTGCCTTGTTGCAGGAAGAAGTGAGCTAATTAATACATATAGGCTCGAACACGCAAAGCATGTTACACGTATATCATGCGCAGTGAATGTTAGCTATTATTATTAATTGTATTCTTTTTTTCCTTTCCTGTTCCGTCTTCGCTGGCTCCCAACAAGTTTTCCTCTGGCCAGGACATGAGCGGGTTCAGCTGCTGCCAAGTCACTGCCAGCCTCAAGTTAGTTTTAGCCATGGATCTGTGGCTTATTTGGCAACAAGCCAATGTGACTCTGGGAGTTTCGTTATGCTTAAGGCTTTCCCCGTCTTTCCCAATTTGTTTTCACATTTTATGTTTCCCTGATGCCCTACGTTTCGTTGTTCATTTCCCTGCTAAAATCATTTTTAGAGGCATCTGTCTCCCGCCAGCCTCGGTTGCTTAGGGGCCCCGTTGTCCTGAGACCTGCTTTCTCTGCGGCCATTCCGAGGCGCCGGGCATTGAGACCCAGGTGTCTCAGCCTGTCGGGTTCTCAGGGAAAGCTGTGGGAAAGTTGTTCTGGCATTGCACTGTTTGTGGGATGAGCTCAGTTGGCTTGTGGTGTGGTGGTCACACAGCGACAGGTGTTTCTCAGAGTCCCTTCCCATGCTGCCCCCATATAGCTGGAGAGTGCCTTGTCTAGGAGCGGAGGAGTTTCCTGGAGATGGAGTAACATCCCCTGCCAGAAAGCACTTAAGAGACCTGTTCCAGCAAACACTCACGGACGGCTGCTGTGGCCAGTGCTGCTGGCCTGGTGTCTGTTTTGACCTACAGTGCGCACTTTATTTTTTTGTGACATCGGAACGTCTCTGCACCTGTATTTTACTCTGCTGTTAAGTCCTGAGTCAGCTCTTAACTGCTACTACACCTTTCTGGTGTCCATACTATACTGCTGTTACTTCAGCCTGGGAGTGGGATTGGAGCCCTCTGAGCAGCAGGCACCACACCCTGTCCTTGCCTGGTCTGTGTCAAATCTTCTGAGTGCAAAGTGCTTTGTACGTAAAGCACTCGGGTAGCCGTCACCCCTGCCCTTGGTGTCTACTTGGCACTGAGCTTTGGGCCAGAGCCTCTCCCAGGTCTGTAGGAATGGAGCTGCCTTTTCTCATCTCCTTCCTCAGTCTGCCTTCCTTTCTTTGGCAAATTTGCGTGTTTTCTTGTACAGCTTAGCTGGGCTCTCTTTTACCTGATTTGCTTGGTGTGGACTCACAACTTTGACCTCAAAGCCCTTTTCCTTGGGGTTGGGTTGCTGTAGGCTTATGATCAGGGGCTTTTGTCTCATGGTGAGATCTTTGCAGAAGGGACACAGTCAGTCTGTTGCTTAATGGGACTGTAGATGTTAAGAGTGGCATCCTGGCACAAGACCAGTATTGACAATGACAGCGAGAGAAGCGGCCTTTTAATTCAGACCCTACCCCGTACTTTCATAAGATGAAGTTTATTAAAGAGAACACCAGTCTGAAAAGCCAACAGGTGTATACTGTGACCCGTGCTTAGCAGCACAAGAAAGCGCTTCCTGTCCCGAGTGAGGGAGTGCATTGCATCTCTGTGGCTCTGTACACTGAGCAGAGCATCTGGATCCAGGCGCATGCTGCTCGTGATACATGGCAGGGCTTCCTGGTACACACATCCTCACATGGCAGTGGGCTGAGGACAAGGCCGGAGAGGGAAGCAGCTGTGTGGCCCTGGCTGCCAGACAGGGTGCTGTACGGTCAGTCAGCCTCGTCGATTCGGATGGCAAGGGCCCATGAGTCAGGGGTGCTGCCTCCCCACAGTTTGCTTATCTTTGCTGTCTGTGATGAGTTAGGGTGCTTTCTTAGAAGGTGGGCACAAGCTGAGTCTTGATGGCAGTGAAAACAGGGTTGGTTCTGTCTTTCCACAGAAACTTGCTTCCAGGGCTGACGGCATCCTGTGACGTGGGACAACAGGGCTCTAGTGTTCCACTCCTAGATGTTTGCAGGCCTGCATTTCTGCCTGCTGTCAGCCAAAGTGGACCTTGCTCTCACCACCCGCCTGCCCCATGTGCTAGCACTTCAGGAGATTGGCCGCTTCTTTAGCAGTTAGTTTAGAAGATAGTGACCTCTACCGGGTGGTTCTAGATTCTGCCTTGAGGTTAATTGGCTAATGAAGTTTTGTTTTAAAACATGGGCTCGAAAGAGAGCTCTCCGTAGTGGCTTGTCATTCCCTGAAGGATTTCCAAGAGCCTGTGTTCAGCAGCCCTTGGTGAATTGAGAGGTCTTGGAGAGGGGAGCGGTTGTGTTTTGTGCAACAGTTATGTTGAGTCGATACAATCACTGCACCCTCTGCTTGTGTCGGCTGAAGGAGCTGGAGCCCACTTCAGTCCTGGGCGAGGGGAAGGAGTGTCGGGTGGAGTGAAGGGTTTCTGTAACAGGGCACTCTTACTCTGTTGATACCGTGACCTTGTTATGGGCAGCTCCATGGTGCCCTTGCAGCTGCCAGTGCTCTGAAATGAATGCCTGTGCCACTGTCCCTTTCTCGTCTCCCCAG
Seq C2 exon
GTGTTTAGGACCGACCTGATCACTGCCATGAAGTTGCATGACTCCTACCAGCTGAACCCGGATGACTACTACGTGCTGGCTGATCCCTGGAGACAGGAGTGGGAGAAAGGGGTCCAGGTGCCTGTGAGCCCAGGGACCATCCCACAGCCTGTGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025764-Phf17:NM_001130186:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=0.294
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF105134=EPL1=PU(10.5=53.3)

							
A:
NA

							
C2:
PF105134=EPL1=FE(34.2=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000026865





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000026865f1775A
          









    
Other Skipping Isoforms:
ENSMUSP00000127113, ENSMUSP00000128152, ENSMUSP00000131441
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr4:128843039-128846374 
LOW PSI
HsaINT0123938
(JADE1)
Human
(hg19)
chr4:129764194-129767529 
LOW PSI
HsaINT0123938
(PHF17)
Rat
(rn6)
chr2:128486297-128488903 
LOW PSI
RnoINT0076930
(Jade1)
Cow
(bosTau6)
chr17:29390656-29392772 
LOW PSI
BtaINT0078756
(JADE1)
Chicken
(galGal4)
chr4:34015629-34018978 
ALTERNATIVE
GgaINT0070274
(JADE1)
Chicken
(galGal3)
chr4:35713478-35716827 
LOW PSI
GgaINT0070274
(PHF17)
Zebrafish
(danRer10)
chr17:26813486-26814196 
ALTERNATIVE
DreINT0083903
(jade1)
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"