PHF1 (PHD finger protein 1)

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Gene miRNA Gene ontology Other IDs Protein Pathways Related genes Diseases linked via similar genes

Gene

• Entrez ID: 5252
• Gene name: PHD finger protein 1
• Gene symbol: PHF1
• Synonyms (NCBI Gene): MTF2L2, PCL1, PHF2, TDRD19C, hPHF1
• Chromosome: 6
• Chromosome location: 6p21.32
• Summary: This gene encodes a Polycomb group protein. The protein is a component of a histone H3 lysine-27 (H3K27)-specific methyltransferase complex, and functions in transcriptional repression of homeotic genes. The protein is also recruited to double-strand brea

miRNA Show/Hide all (116)

miRTarBase ID	miRNA	Experiments	Reference
MIRT615541	hsa-miR-136-3p	HITS-CLIP	23824327
MIRT615540	hsa-miR-622	HITS-CLIP	23824327
MIRT615539	hsa-miR-5196-3p	HITS-CLIP	23824327
MIRT615538	hsa-miR-4793-5p	HITS-CLIP	23824327
MIRT615537	hsa-miR-1470	HITS-CLIP	23824327
MIRT615536	hsa-miR-4667-3p	HITS-CLIP	23824327
MIRT615535	hsa-miR-5193	HITS-CLIP	23824327
MIRT615534	hsa-miR-4264	HITS-CLIP	23824327
MIRT615533	hsa-miR-4469	HITS-CLIP	23824327
MIRT615532	hsa-miR-6749-3p	HITS-CLIP	23824327
MIRT615541	hsa-miR-136-3p	HITS-CLIP	23824327
MIRT615540	hsa-miR-622	HITS-CLIP	23824327
MIRT615539	hsa-miR-5196-3p	HITS-CLIP	23824327
MIRT615538	hsa-miR-4793-5p	HITS-CLIP	23824327
MIRT615537	hsa-miR-1470	HITS-CLIP	23824327
MIRT615536	hsa-miR-4667-3p	HITS-CLIP	23824327
MIRT615535	hsa-miR-5193	HITS-CLIP	23824327
MIRT615534	hsa-miR-4264	HITS-CLIP	23824327
MIRT615533	hsa-miR-4469	HITS-CLIP	23824327
MIRT615532	hsa-miR-6749-3p	HITS-CLIP	23824327
MIRT615541	hsa-miR-136-3p	HITS-CLIP	23824327
MIRT615540	hsa-miR-622	HITS-CLIP	23824327
MIRT615539	hsa-miR-5196-3p	HITS-CLIP	23824327
MIRT615538	hsa-miR-4793-5p	HITS-CLIP	23824327
MIRT615537	hsa-miR-1470	HITS-CLIP	23824327
MIRT615536	hsa-miR-4667-3p	HITS-CLIP	23824327
MIRT615535	hsa-miR-5193	HITS-CLIP	23824327
MIRT615534	hsa-miR-4264	HITS-CLIP	23824327
MIRT615533	hsa-miR-4469	HITS-CLIP	23824327
MIRT615532	hsa-miR-6749-3p	HITS-CLIP	23824327
MIRT615536	hsa-miR-4667-3p	PAR-CLIP	26701625
MIRT615536	hsa-miR-4667-3p	PAR-CLIP	26701625
MIRT615535	hsa-miR-5193	PAR-CLIP	26701625
MIRT615535	hsa-miR-5193	PAR-CLIP	26701625
MIRT615532	hsa-miR-6749-3p	PAR-CLIP	26701625
MIRT615532	hsa-miR-6749-3p	PAR-CLIP	26701625
MIRT615541	hsa-miR-136-3p	HITS-CLIP	23824327
MIRT615540	hsa-miR-622	HITS-CLIP	23824327
MIRT615539	hsa-miR-5196-3p	HITS-CLIP	23824327
MIRT615538	hsa-miR-4793-5p	HITS-CLIP	23824327
MIRT615537	hsa-miR-1470	HITS-CLIP	23824327
MIRT615536	hsa-miR-4667-3p	HITS-CLIP	23824327
MIRT615535	hsa-miR-5193	HITS-CLIP	23824327
MIRT615534	hsa-miR-4264	HITS-CLIP	23824327
MIRT615533	hsa-miR-4469	HITS-CLIP	23824327
MIRT615532	hsa-miR-6749-3p	HITS-CLIP	23824327
MIRT615541	hsa-miR-136-3p	HITS-CLIP	23824327
MIRT615540	hsa-miR-622	HITS-CLIP	23824327
MIRT615539	hsa-miR-5196-3p	HITS-CLIP	23824327
MIRT615538	hsa-miR-4793-5p	HITS-CLIP	23824327
MIRT615537	hsa-miR-1470	HITS-CLIP	23824327
MIRT615536	hsa-miR-4667-3p	HITS-CLIP	23824327
MIRT615535	hsa-miR-5193	HITS-CLIP	23824327
MIRT615534	hsa-miR-4264	HITS-CLIP	23824327
MIRT615533	hsa-miR-4469	HITS-CLIP	23824327
MIRT615532	hsa-miR-6749-3p	HITS-CLIP	23824327
MIRT615541	hsa-miR-136-3p	HITS-CLIP	23824327
MIRT615540	hsa-miR-622	HITS-CLIP	23824327
MIRT615539	hsa-miR-5196-3p	HITS-CLIP	23824327
MIRT615538	hsa-miR-4793-5p	HITS-CLIP	23824327
MIRT615537	hsa-miR-1470	HITS-CLIP	23824327
MIRT615536	hsa-miR-4667-3p	HITS-CLIP	23824327
MIRT615535	hsa-miR-5193	HITS-CLIP	23824327
MIRT615534	hsa-miR-4264	HITS-CLIP	23824327
MIRT615533	hsa-miR-4469	HITS-CLIP	23824327
MIRT615532	hsa-miR-6749-3p	HITS-CLIP	23824327
MIRT1230021	hsa-miR-106a	CLIP-seq
MIRT1230022	hsa-miR-106b	CLIP-seq
MIRT1230023	hsa-miR-1257	CLIP-seq
MIRT1230024	hsa-miR-1294	CLIP-seq
MIRT1230025	hsa-miR-17	CLIP-seq
MIRT1230026	hsa-miR-188-5p	CLIP-seq
MIRT1230027	hsa-miR-194	CLIP-seq
MIRT1230028	hsa-miR-20a	CLIP-seq
MIRT1230029	hsa-miR-20b	CLIP-seq
MIRT1230030	hsa-miR-2392	CLIP-seq
MIRT1230031	hsa-miR-3650	CLIP-seq
MIRT1230032	hsa-miR-3689a-3p	CLIP-seq
MIRT1230033	hsa-miR-3689c	CLIP-seq
MIRT1230034	hsa-miR-371-3p	CLIP-seq
MIRT1230035	hsa-miR-3925-3p	CLIP-seq
MIRT1230036	hsa-miR-4257	CLIP-seq
MIRT1230037	hsa-miR-4497	CLIP-seq
MIRT1230038	hsa-miR-4533	CLIP-seq
MIRT1230039	hsa-miR-4705	CLIP-seq
MIRT1230040	hsa-miR-4710	CLIP-seq
MIRT1230041	hsa-miR-4713-3p	CLIP-seq
MIRT1230042	hsa-miR-4728-5p	CLIP-seq
MIRT1230043	hsa-miR-4747-5p	CLIP-seq
MIRT1230044	hsa-miR-4753-3p	CLIP-seq
MIRT1230045	hsa-miR-4768-5p	CLIP-seq
MIRT1230046	hsa-miR-4797-5p	CLIP-seq
MIRT1230047	hsa-miR-485-3p	CLIP-seq
MIRT1230048	hsa-miR-487a	CLIP-seq
MIRT1230049	hsa-miR-495	CLIP-seq
MIRT1230050	hsa-miR-519d	CLIP-seq
MIRT1230051	hsa-miR-766	CLIP-seq
MIRT1230052	hsa-miR-873	CLIP-seq
MIRT1230053	hsa-miR-93	CLIP-seq
MIRT2067341	hsa-miR-1285	CLIP-seq
MIRT2067342	hsa-miR-3187-5p	CLIP-seq
MIRT2067343	hsa-miR-4320	CLIP-seq
MIRT2067344	hsa-miR-593	CLIP-seq
MIRT2067345	hsa-miR-612	CLIP-seq
MIRT2067346	hsa-miR-661	CLIP-seq
MIRT1230024	hsa-miR-1294	CLIP-seq
MIRT1230036	hsa-miR-4257	CLIP-seq
MIRT2067343	hsa-miR-4320	CLIP-seq
MIRT1230040	hsa-miR-4710	CLIP-seq
MIRT1230024	hsa-miR-1294	CLIP-seq
MIRT2392460	hsa-miR-3675-3p	CLIP-seq
MIRT1230035	hsa-miR-3925-3p	CLIP-seq
MIRT1230036	hsa-miR-4257	CLIP-seq
MIRT2392461	hsa-miR-4640-3p	CLIP-seq
MIRT1230040	hsa-miR-4710	CLIP-seq
MIRT1230051	hsa-miR-766	CLIP-seq

Gene ontology (GO) Show/Hide all (28)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001222	Function	Transcription corepressor binding	IPI	29628311
GO:0003677	Function	DNA binding	IBA
GO:0003682	Function	Chromatin binding	IBA
GO:0003682	Function	Chromatin binding	IEA
GO:0005515	Function	Protein binding	IPI	11571280, 16189514, 21516116, 23142980, 24981860, 25416956, 26496610, 27705803, 29628311, 31515488, 32296183, 33961781, 34591612
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	23273982
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	20873783
GO:0005813	Component	Centrosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005856	Component	Cytoskeleton	IEA
GO:0006325	Process	Chromatin organization	IEA
GO:0006974	Process	DNA damage response	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0035098	Component	ESC/E(Z) complex	IDA	23273982
GO:0035861	Component	Site of double-strand break	IDA	23142980
GO:0042802	Function	Identical protein binding	IPI	29628311
GO:0045814	Process	Negative regulation of gene expression, epigenetic	IBA
GO:0046872	Function	Metal ion binding	IEA
GO:0140002	Function	Histone H3K4me3 reader activity	IDA	23142980
GO:0140003	Function	Histone H3K36me3 reader activity	IDA	23142980, 23273982
GO:0140861	Process	DNA repair-dependent chromatin remodeling	IDA	23142980
GO:1990226	Function	Histone methyltransferase binding	IPI	29628311

Other IDs

• MIM: 602881
• HGNC: 8919
• e!Ensembl: ENSG00000112511

Protein

• UniProt ID: O43189
• Protein name: PHD finger protein 1 (Protein PHF1) (hPHF1) (Polycomb-like protein 1) (hPCl1)
• Protein function: Polycomb group (PcG) that specifically binds histone H3 trimethylated at 'Lys-36' (H3K36me3) and recruits the PRC2 complex. Involved in DNA damage response and is recruited at double-strand breaks (DSBs). Acts by binding to H3K36me3, a mark for
• PDB: 2E5P , 2M0O , 4HCZ , 5XFN , 5XFO , 5XFP , 6WAT , 6WAV , 7LKY , 8H43
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00628	PHD	89 → 142	PHD-finger	Domain
  PF14061	Mtf2_C	530 → 565	Polycomb-like MTF2 factor 2	Domain
  PF18104	Tudor_2	34 → 69	Jumonji domain-containing protein 2A Tudor domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Highest levels in heart, skeletal muscle, and pancreas, lower levels in brain, placenta, lung, liver and kidney.
• Sequence:

  MAQPPRLSRSGASSLWDPASPAPTSGPRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREV
  CLVQFEDDSQFLVLWKDISPAALPGEELLCCVCRSETVVPGNRLVSCEKCRHAYHQDCHV
  PRAPAPGEGEGTSWVCRQCVFAIATKRGGALKKGPYARAMLGMKLSLPYGLKGLDWDAGH
  LSNRQQSYCYCGGPGEWNLKMLQCRSCLQWFHEACTQCLSKPLLYGDRFYEFECCVCRGG
  PEKVRRLQLRWVDVAHLVLYHLSVCCKKKYFDFDREILPFTSENWDSLLLGELSDTPKGE
  RSSRLLSALNSHKDRFISGREIKKRKCLFGLHARMPPPVEPPTGDGALTSFPSGQGPGGG
  VSRPLGKRRRPEPEPLRRRQKGKVEELGPPSAVRNQPEPQEQRERAHLQRALQASVSPPS
  PSPNQSYQGSSGYNFRPTDARCLPSSPIRMFASFHPSASTAGTSGDSGPPDRSPLELHIG
  FPTDIPKSAPHSMTASSSSVSSPSPGLPRRSAPPSPLCRSLSPGTGGGVRGGVGYLSRGD
  PVRVLARRVRPDGSVQYLVEWGGGGIF

• Sequence length: 567

Pathways

KEGG Pathway:

Polycomb repressive complex

Reactome Pathway:

PRC2 methylates histones and DNA

Related Genes

Sort by: Blended Diseases Pathways Evidence source

MTF2 2 shared pathwaysPolycomb repressive complex, PRC2 methylates histones and DNA Related via 2 shared pathways including Polycomb repressive complex, PRC2 methylates histones and DNA. PHF19 2 shared pathwaysPolycomb repressive complex, PRC2 methylates histones and DNA Related via 2 shared pathways including Polycomb repressive complex, PRC2 methylates histones and DNA. AEBP2 2 shared pathwaysPolycomb repressive complex, PRC2 methylates histones and DNA Related via 2 shared pathways including Polycomb repressive complex, PRC2 methylates histones and DNA. JARID2 2 shared pathwaysPolycomb repressive complex, PRC2 methylates histones and DNA Related via 2 shared pathways including Polycomb repressive complex, PRC2 methylates histones and DNA. EED 2 shared pathwaysPolycomb repressive complex, PRC2 methylates histones and DNA Related via 2 shared pathways including Polycomb repressive complex, PRC2 methylates histones and DNA.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
MTF2	0	[]	2	["Polycomb repressive complex","PRC2 methylates histones and DNA"]	0	[]
PHF19	0	[]	2	["Polycomb repressive complex","PRC2 methylates histones and DNA"]	0	[]
AEBP2	0	[]	2	["Polycomb repressive complex","PRC2 methylates histones and DNA"]	0	[]
JARID2	0	[]	2	["Polycomb repressive complex","PRC2 methylates histones and DNA"]	0	[]
EED	0	[]	2	["Polycomb repressive complex","PRC2 methylates histones and DNA"]	0	[]

Diseases Linked via Similar Genes

Autism Linked via 2 of 5 related genesJARID2, EED Breast cancer Linked via 1 of 5 related genesMTF2 Insomnia Linked via 1 of 5 related genesMTF2 Oligodendroglioma Linked via 1 of 5 related genesMTF2 Parkinson disease Linked via 1 of 5 related genesMTF2

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Autism	2	["JARID2","EED"]
Breast cancer	1	["MTF2"]
Insomnia	1	["MTF2"]
Oligodendroglioma	1	["MTF2"]
Parkinson disease	1	["MTF2"]