Special

MmuINT0118749 @ mm9

Intron Retention

Gene
ENSMUSG00000025764 | Phf17
Description
PHD finger protein 17 [Source:MGI Symbol;Acc:MGI:1925835]
Coordinates
chr3:41400537-41404111:+
Coord C1 exon
chr3:41400537-41400748
Coord A exon
chr3:41400749-41403943
Coord C2 exon
chr3:41403944-41404111
Length
3195 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ACAAAGTTGTGGCCTTACAGGCT
3' ss Score
5.07
Exon sequences
Seq C1 exon
GGATGCCGGAGCTGGACGAGTACACCATGGAAAGGGTCTTGGAGGAATTCGAACAGCGATGCTATGACAATATGAATCATGCCATAGAGACAGAAGAGGGCTTGGGGATTGAATACGACGAAGACGTTGTCTGCGATGTCTGCCAGTCACCTGATGGCGAGGACGGCAACGAGATGGTGTTCTGTGACAAGTGTAACATCTGTGTGCACCAG
Seq A exon
GTGAGTGGGGCAGCAGAGCCCAGAGAGAGCTGGGTGCCGTTCTGGTGCTGAGCCTCTCAGCCAGCCTGTACTGCCTGGAGTCTAGGGTGGTTCTTCCTAATGGAGCCGCATCCCACAGTTGTGCTTTAGGAAAGTCTTACCTGACTGTAATCCCAGGGCATGGCTCTCTGCCTTTACTCCACGAAGGCACTGCGATTCAACTGGGAACACTGGAAACAAACCCGAGCAAAGGGTGCTTAAACTCTACGTTAGCTTTTAACTGCGGTGACTAAAACAACAGAAGCTGTCTCTGGAACTGGAGTTTTGTTCTTCCTTGTCTCTTCCTAGCTCATGGTGGATTCTTGTCAGTCCTTGGTGGTTGGCTTGCCCATTAGTCTTCACGATGTCTTCCCTGTGTGTCTGTCTAGATAGGGTTATCTTCTCACACAGTCCTGGTCCTGTTGGATTAGGTGCCTGCCTGCACAGTGTGGTCTCAGTTTACATAGTTGTGTGTCACAACTGTTTCTAAAGGTCCCGTTTTCAGGTGGTGGTGCGGTCCTAAAGTATCTTCTGGGGGATACAGGATAAACCATAGCGTTCATGTGTTTACGTATCAGCTTAGCTGTGGAAGGGGGTCAGGCACCCCTTTGACTTTTCGTCTTAGATTTTGGTTAGTTCTGTGTATGAATATTGTGCATGTGTATGTCTGTGCACCACCTAGAACGACTGGTGCCCAGAGGTCAGAAGAGCACGTCAGGGGTCTCCGCTGGAATTGGAGCTCTGCGATGGCTGTAAGACACTGCCTGTGCTGGGAACTCTGAGTAGTCAGTGCTCTTAACTGCTGAGCCGTCTCTGACTCCCTTTTCGTGAGCATTATTTCAAGGTGGCAGTAGACCCACCTTGGTGGGGGCTTGCTGTTGTCTTTTAGTGAAGGTAATTTAGAAAGCTTAAGCATAGATACAGGGGCCTTTTACCCCTCATGTAACTTAACAGATTTATTATTACTTTGTGGTGGTGTGTGTGTCTGTCTATCTGTCTGTCTGTGTGAATGCTGGAGGAAGTGAAAGTTGGATCCCCTCAGCTGGGCATATAGGTTGTGAGATATCTGATATAGGTGCTGTGAGCCACACTGGGGTCCTTGAAGGGCAGCAAGTGCCTTTAACCACACAGCTGTCTGTCTGTCGAGTTCTGTATTTGACTTTGAATGTGGTGGTCAAGTGATGTGGATTTGCGTGGGGACATGTGTACCAGGCAGTTTTGTGATTTAGAAAACTGTCCTGACGTACTTTTCTGTGAGGCCATCAGTGACTCTCGGAGAAAGTGGAAAGTTGCTTGTGTGACCTGAGCTCTGTGTTTTATTATTGTTCTTTAAAATAGCCCTGGCTGCCTGTATCTCAGTGTATAGGCCAGGATAGCCTCCAACTGAGATAATCCTCCTGCCTCTGCCGCTGAGTGCTGAGATCACACATACTCACTGCCACACTCAGAGATCTGGGTTACCCCTTTCTCTATAATTCACCTCTAGGGCTTTAGAAAACTCCATGGCTTCACCAGCGGTGGCCCCGTCTCAGCTCATCTTCACAGGGAACCCTGAGACGGACCTGTTTTGTATCTGGGCTTTGTGGTCCAGAGGGCGTCTTGCCCTGGAGTCCCTGTGGAGGTGTGTGTGATGGGAGGCCACACGACTGCCACTGTTGCTGCTGCCTCTCATTGACCTAGTGACCCTGAAGTCTTCTGACATTTGCTGTTACGAGATTTCTGCTTGAAATCCAGTTGTGCTCTGTGCTTCAGAAGTCTGTAAGCTGCCATCAGGGCTGTGTGCCAACACCTTAGCATGTGGGTGGCAGAGTTGGCCCTGATGACTTCCGCTTCTTCTGCTCTCGACACTTCACGCTCACTTTATTTTACTTTCCGTGAGATTCTTCATGGCTTGTCTTTAAGGCATACTTGATTAGTGTAGATGTGCCTTTCCAGTAAACGAGATCCTCGCTTCAAAGGGAGCTCTAGAACGCCATGGCGTTTGAAGCCCTCCTACTACTGTTGAGATCTGTAAGAACACTGCTTTGCTGGTAGACTTGTTGACCACTGCTCATTCGTGGCCGCGCGGAGCTCTCAGGACTGCGGTGTTACTGTTTCTTTGCTGAGCTCCGCTCTCATCCTTGTGTTTTCCTTCTTGTGTCCTGGGCGTTCGGATTTCATGGTGGCTGTGCTGTTTCTGCCTGGAGAAATAGAGCCAGGTTCCTGTGACTTCCGACTTGCAGTTCATTTAAGGATAACGTTGTGAACTGTCTGGGTTTTAAAGGGCTGTCTGAGCACACTCCCGGTACTACCATGGGTTTGTTTATTTACTCCCCTTATTGAAACATTTGCTTTTTCTTTCTTTAAACCAGCATAATGATTTCAGTTGTAAAAGCCTTAATTTCTGCAGTTTGGGTTGTCTTGTGTAATTTTGCCAACTTGTGCAAAACAGGCTTTGTTTTTAAACATCAGCGAAAGAAACCAAACTCTCATTTTGAAATGTCTCGCTCTTCTGCGGCTGTCTGTTCGCATGAACTCTGTTGGACTCCAGTAGGAGGAGTGTGTCCAGCTTGAGCAGCGAATGGTTGCCCAGCCACTATCACCTTGGCTTTGGTGCTTTGTTTTGCCTTCGTTCCGTGTCACGCCCATCATGAAAGCAGAGAGAGGTCTGTTGTACCCTCTTGAAGCCTGCAGCCAGGTTGGAGCATTGGCTGCTCAGTGGTTGGAACTGTCTTATGGCTGGGTCTCTTCCGCACCACAGCAACACTCGTTATTTTAGGATCCCTCTTGTCAAGTTCTTGGGACTTCCTGTGCTGAAGACACATGTGGCGTGTCTTTGGAGCTCAGGCACATGGGTGCTTGGAGGTGGGCTGGCATATTTCCTCGAGGGTCAGGATCACAGTTAGGTGGATATGGGCATGTCTACTTTGGTGTGGCTCTGTGAAAATCCTTCTAGATTGTTTTTCAGTTCACAAATAGGGGCTGGGCGATGCCTCGTAAGACTTGCTGACCGCCCTTCAAGAGAACAAAGGCTTGATTCCTAGATCCCACATTGGCTGCTTACAGCAGGCCATTACTCCAGTTCTAGGGGATCCAGCACCCTCTTTTGGCCTCTGTGGGCATTACACAGTGTGTGGCACAGTGATATATAGAGGCAAGACACCCATACACATAAATAACAAAGTTGTGGCCTTACAG
Seq C2 exon
GCTTGCTATGGGATCCTCAAGGTGCCAGAGGGCAGTTGGCTATGTCGTACATGTGCCCTGGGAGTTCAGCCAAAATGTTTGCTGTGTCCCAAGAAAGGCGGAGCTATGAAGCCGACCCGCAGCGGAACCAAGTGGGTCCACGTCAGCTGTGCCCTGTGGATCCCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025764-Phf17:NM_001130186:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.014 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF105134=EPL1=PD(12.5=26.8),PF0013017=C1_1=PU(75.9=62.0),PF138311=PHD_2=PU(42.9=21.1)

							
A:
NA

							
C2:
PF0013017=C1_1=PD(20.7=21.4),PF138311=PHD_2=PD(51.4=32.1),PF138321=zf-HC5HC2H_2=PU(28.3=57.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000026865





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000127113, ENSMUSP00000128152, ENSMUSP00000131441
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr4:128852269-128855629 
ALTERNATIVE
HsaINT0123941
(JADE1)
Human
(hg19)
chr4:129773424-129776784 
ALTERNATIVE
HsaINT0123941
(PHF17)
Rat
(rn6)
chr2:128494196-128497238 
LOW PSI
RnoINT0076933
(Jade1)
Cow
(bosTau6)
chr17:29383293-29385946 
LOW PSI
BtaINT0078759
(JADE1)
Chicken
(galGal4)
chr4:34025852-34026971 
ALTERNATIVE
GgaINT0070277
(JADE1)
Chicken
(galGal3)
chr4:35723701-35724820 
ALTERNATIVE
GgaINT0070277
(PHF17)
Zebrafish
(danRer10)
chr17:26814940-26822351 
LOW PSI
DreINT0083906
(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"