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PHF13 Gene

protein-coding GIFtS: 42

GC01P005821

PHD finger protein 13
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
About This Section

Aliases & Descriptions
PHD finger protein 13¹ ²
MGC43399¹ ²
SPOC1²
PHD zinc finger protein PHF5²
survival time-associated PHD protein in ovarian cancer²
PHF5²

External Ids:	HGNC: 22983¹	Entrez Gene: 148479²	Ensembl: ENSG00000116273⁷	UniProtKB: Q86YI8³

Export aliases for PHF13 gene to outside databases

Previous GC identifers: GC01P006270 GC01P006383 GC01P006608 GC01P006596 GC01P006673

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the PHF13 gene promoter:
         SRF   Bach2   LCR-F1   c-Myb   TBP   Pax-6   MEF-2A   Fra-1   AP-1   c-Jun
         Other transcription factors

Search SABiosciences Chromatin IP Primers for PHF13

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for PHF13

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p36.31 Ensembl cytogenetic band: 1p36.31 HGNC cytogenetic band: 1p36.23

PHF13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PHF13 gene location

GeneLoc gene densities for chromosome 1 GeneLoc Exon Structure

GeneLoc location for GC01P005821: view genomic region (about GC identifiers)

Start:	5,821,676 bp from pter
End:	5,831,583 bp from pter
Size:	9,908 bases
Orientation:	plus strand

1 alternative location:

Chr1+ 6,673,745-6,684,093

RefSeq DNA sequence:

NC_000001.10 NT_021937.19

(According to ¹UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
About This Section

UniProtKB/Swiss-Prot: PHF13_HUMAN, Q86YI8 (See protein sequence)

Recommended Name: PHD finger protein 13

Size: 300 amino acids; 33582 Da

Sequence caution: Sequence=AAH32792.2; Type=Erroneous initiation;

Secondary accessions: Q5TH65 Q8N551 Q9UJP2

Explore the universe of human proteins at neXtProt for PHF13: NX_Q86YI8

REFSEQ proteins: NP_722519.2

ENSEMBL proteins:

ENSP00000366876

Human Recombinant Proteins

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Antibodies for PHF13:

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	Browse antibodies at Epitomics

Assays for PHF13:

	Browse Kits and Assays available from Millipore
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	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	Browse R&D Systems for biochemical assays
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	Uscn ELISAs and CLIAs for PHF13

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

PHF13 for domains About GeneDecksing

4 InterPro domains/families:

IPR001965 Znf_PHD

IPR013083 Znf_RING/FYVE/PHD

IPR011011 Znf_FYVE_PHD

IPR019787 Znf_PHD-finger

Graphical View of Domain Structure for InterPro Entry Q86YI8

ProtoNet protein and cluster: Q86YI8

1 Blocks protein family: IPB001965 Zn-finger-like

UniProtKB/Swiss-Prot: PHF13_HUMAN, Q86YI8

Similarity: Contains 1 PHD-type zinc finger

(According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
About This Section

Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Browse Nano Scale siRNA at Sigma-Aldrich Sigma-Aldrich siRNA Panels and esiRNA and siRNA for PHF13 Sigma-Aldrich shRNA for PHF13
		OriGene 29mer shRNA kits in GFP-retroviral vector: PHF13 OriGene shRNA RFP: PHF13 OriGene basic RS shRNA: PHF13 OriGene siRNA: PHF13
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of PHF13

miRNA:		Sigma-Aldrich microRNA Mimics for PHF13 Browse microRNA target validation systems at Sigma-Aldrich
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PHF13
		8/9 SABiosciences Assays for microRNAs that regulate PHF13 (see all 9):
		hsa-miR-448 hsa-miR-517a hsa-miR-1301 hsa-miR-517b hsa-miR-182 hsa-miR-582-5p hsa-miR-19b hsa-miR-1207-5p

Gene
Editing:

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		OriGene GFP tagged cDNA clones in CMV expression vector: PHF13 OriGene Myc/DDK tagged cDNA clones in CMV expression vector: PHF13 OriGene untagged cDNA clones in CMV expression vector: PHF13 OriGene 3'-UTR clone: PHF13 Browse MicroRNA Expression Plasmids
		GenScript Custom cDNA clone Services for PHF13
		Browse Sino Biological Human cDNA Clones

Cell
Lines:

GenScript Custom overexpressing Cell Line Services for PHF13

3 Gene Ontology (GO) molecular function terms (GO ID links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005515	protein binding	IEA	--
GO:0008270	zinc ion binding	IEA	--
GO:0046872	metal ion binding	IEA	--

About this table

PHF13 for ontologies About GeneDecksing

(Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
About This Section

SABiosciences Pathway-Focused PCR Array including PHF13: PAHS-086A

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for PHF13

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse Small Molecules at Sigma-Aldrich

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for PHF13

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Millipore,
siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
About This Section

Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Browse Nano Scale siRNA at Sigma-Aldrich Sigma-Aldrich siRNA Panels and esiRNA and siRNA for PHF13 Sigma-Aldrich shRNA for PHF13
		OriGene 29mer shRNA kits in GFP-retroviral vector: PHF13 OriGene shRNA RFP: PHF13 OriGene basic RS shRNA: PHF13 OriGene siRNA: PHF13
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of PHF13

miRNA:		Sigma-Aldrich microRNA Mimics for PHF13 Browse microRNA target validation systems at Sigma-Aldrich
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PHF13
		8/9 SABiosciences Assays for microRNAs that regulate PHF13 (see all 9):
		hsa-miR-448 hsa-miR-517a hsa-miR-1301 hsa-miR-517b hsa-miR-182 hsa-miR-582-5p hsa-miR-19b hsa-miR-1207-5p

Clones:		Browse FLAG tag genes at Sigma-Aldrich
		OriGene GFP tagged cDNA clones in CMV expression vector: PHF13 OriGene Myc/DDK tagged cDNA clones in CMV expression vector: PHF13 OriGene untagged cDNA clones in CMV expression vector: PHF13 OriGene 3'-UTR Clone: PHF13 Browse OriGene MicroRNA Expression Plasmids
		GenScript Custom cDNA clone Services for PHF13

Primers:		OriGene genome-wide validated SYBR primer pairs: PHF13 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay for PHF13: PPH07499A

REFSEQ mRNAs for PHF13 gene:

NM_153812.2

Additional cDNA sequence:

AB209544.1 AK027492.1 AK097715.1 AK315110.1 AL121733.1 AY069975.1 BC007931.1 BC032792.2

BC038516.1 BC048202.1 CR612215.1 CR618324.1

10 DOTS entries:

DT.417354 DT.100025755 DT.91747043 DT.121348563 DT.100737309 DT.100778437 DT.121348573 DT.95274331

DT.100737310 DT.100778442

24/195 AceView cDNA sequences (see all 195):

CR612215 AI907377 AI589556 CR618324 BQ422271 AI391735 BQ643541 AA933577

BE550598 AA909758 AI825447 BU159681 AI263052 BQ189390 AI014879 BQ649066

AL121733 AA749027 AA860262 AW082091 AI240231 AA243168 BF941228 BQ233357

highest scoring ESTs for PHF13:

T78497 AA143098 AA203440 AA234655 AA398641 AA424543 AA507923 AA719063 AA744679 AA749027

Unigene Cluster for PHF13:

PHD finger protein 13

Hs.516079 [show with all ESTs]

Unigene Representative Sequence: BC038516

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for PHF13

ExUns:	1	^	2a	·	2b	^	3a	·	3b	^	4	^	5	^	6
SP1:			-
SP2:			-		-		-		-		-		-
SP3:
SP4:

About this scheme

ECgene alternative splicing isoforms for PHF13
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000377648(uc001aob.3) ENST00000495385

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Primers from OriGene and/or SABiosciences )
About This Section

PHF13 expression in normal and diseased human tissues

¹ / ² / ³

4 probe-sets matching PHF13 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
84771_at²^{, 3}	U95-E	1	0.62	1.00	0.79	1.19	T78497	1.00	1.00	1.00	1
57218_at²^{, 3}	U95-B	1	0.31	1.00	0.42	0.81	AA203440	0.80	1.00	0.91	1
225005_at²^{, 3}	U133-B	1	0.64	1.00	--	--	AL039384	0.60	1.00	0.82	1
225005_at²	U133Plus2	1	0.64	1.00	--	--	--	--	--	--	--

About this table

PHF13 for expression About GeneDecksing

Data from Genenote (Publications) and GNF BioGPS
About these images

PHF13 gene electronic northern expression

About these images

CGAP SAGE TAG: TGGCACCTTT

SOURCE GeneReport for Unigene cluster: Hs.516079

Primers:		OriGene genome-wide validated SYBR primer pairs: PHF13 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay for PHF13: PPH07499A

SABiosciences Expression via Pathway-Focused PCR Array including PHF13: PAHS-086A

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for PHF13 gene from 5/9 species (see all 9)

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	PHF13¹	--	PHD finger protein 13	90.67(n) 95.67(a)	479592 XM_536730.2 XP_536730.2
chimpanzee (Pan troglodytes)	PHF13¹	--	PHD finger protein 13	99.56(n) 99.67(a)	469786 XM_525170.2 XP_525170.2
cow (Bos taurus)	PHF13¹	--	PHD finger protein 13	89.08(n) 94.43(a)	540889 XM_613592.3 XP_613592.2
rat (Rattus norvegicus)	Phf13¹	--	PHD finger protein 13	88.4(n) 93.92(a)	313742 XM_233700.4 XP_233700.4
mouse (Mus musculus)	Phf13^{1 , 5}	4 (82.81 cM)⁵	PHD finger protein 13^{1, 5}	90.05(n)¹ 95.83(a)¹	230936¹ NM_172705.1¹ NP_766293.1¹ AI428357⁵ AI605405⁵ (see all 12)

About this table Species with no ortholog for PHF13

ENSEMBL Gene Tree for PHF13 (if available)

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

Paralogs for PHF13 gene

PHF23²

PHF13 for paralogs About GeneDecksing

(SNPs according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section

SNP ID	Valid	Chr 1 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
Genomic Data				Transcription Related Data				Allele Frequencies
			--	--	--		--	--
rs14057^1,2	C,F,O,A,H,	6683240(+)	`CCAAGG/AGGCTT`	1	--	ut3¹		16		MN EA NS NA WA	2504
rs200435^1,2	C,	6676928(+)	`TCTTCT/CGAGTT`	1	--	int¹		2		MN WA	234
rs200436^1,2	C,F,	6675489(+)	`AGGAGG/AAGGTT`	1	--	int¹ trp³		14		EA NA NS	726
rs1709853^1,2	--	6677430(+)	`cgtgaC/Ggtacc`	1	--	int¹		0	--	--	--	--
rs1737377^1,2	--	6677431(-)	`cggtaC/Gctcac`	1	--	int¹		0	--	--	--	--
rs2072948^1,2	C,F,	6679848(-)	`CAAAGG/ATGGCA`	1	--	int¹		13		EA NS NA	2422
rs2986981^1,2	--	6674229(+)	`CTCAGC/GCAGCC`	1	--	int¹		0	--	--	--	--
rs3747994^1,2	C,F,A,H,	6681744(-)	`AGCCCA/GCGGTC`	1	--	ut3¹ ese³		17		EA NS NA WA	2484
rs3817873^1,2	C,F,	6676541(-)	`CTCATG/ATGGCA`	1	--	int¹		1		EA	1480
rs5772244^1,2	C	6676106(+)	`tttttT/-gagtt`	1	--	int¹		1		NA	2

About this table

HapMap Linkage Disequilibrium images for PHF13 (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for PHF13: --

QIAGEN SeqTarget long-range PCR primers for resequencing PHF13

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
About This Section

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶UniProtKB/TrEMBL, and/or ⁷Novoseek)
About This Section

8 PubMed articles for PHF13 gene integrated from 7 sources:
(articles sorted by number of sources associating them with PHF13)

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{1, 2} Ota T.... Sugano S. (2004)
SPOC1: a novel PHD-containing protein modulating chro matin structure and mitotic chromosome condensation. (PubMed id 19638409)¹ Kinkley S....Will H. (2009)
hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)¹ Lamesch P.... Vidal M. (2007)
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)¹ Kimura K.... Sugano S. (2006)
The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)² Gregory S.G.... Bentley D.R. (2006)
SPOC1, a novel PHD-finger protein: association with residual disease and survival in ovarian cancer. (PubMed id 15825179)¹ Mohrmann G....Winterpacht A. (2005)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 148479	HGNC: 22983	AceView: PHF13	Ensembl:ENSG00000116273	euGenes: HUgn148479
ECgene: PHF13	H-InvDB: PHF13

(According to HUGE)
About This Section

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Intellectual Property for PHF13 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from XenneX, Inc.)

About This Section

Patent Information for PHF13 gene:
Search GeneIP for patents involving PHF13

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or Enzo Life Sciences)
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	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PHF13
	SeqTarget long-range PCR primers for resequencing PHF13
	QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for PHF13
	QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of PHF13

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PHF13 Gene

protein-coding GIFtS: 42

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PHF13 Gene

protein-coding GIFtS: 42

Aliases & Descriptionsfor PHF13 gene

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