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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

PHTF1 Gene

protein-coding GIFtS: 53
GCID: GC01M114240

putative homeodomain transcription factor 1

(Previous symbol: PHTF)

Explore 1 disease affiliated with
PHTF1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Putative Homeodomain Transcription Factor 1¹ ²
PHTF¹ ² ³

External Ids:	HGNC: 8939¹	Entrez Gene: 10745²	Ensembl: ENSG00000116793⁷	OMIM: 604950⁵	UniProtKB: Q9UMS5³

Export aliases for PHTF1 gene to outside databases

Previous GC identifers: GC01M114653 GC01M113122 GC01M113339 GC01M113538 GC01M113951 GC01M112097

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

UniProtKB/Swiss-Prot: PHTF1_HUMAN, Q9UMS5

Function: May play a role in transcription regulation

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000001.10 NC_018912.1 NT_032977.9

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the PHTF1 gene promoter:
TBP Sox5 AP-1 ATF-2 Lmo2 MIF-1 Nkx2-5 PPAR-gamma1 c-Jun
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: PHTF1 promoter sequence

Search SABiosciences Chromatin IP Primers for PHTF1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PHTF1

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

Entrez Gene cytogenetic band: 1p13 Ensembl cytogenetic band: 1p13.2 HGNC cytogenetic band: 1p13-p11

PHTF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PHTF1 gene location

GeneLoc information about chromosome 1 GeneLoc Exon Structure

GeneLoc location for GC01M114240: view genomic region (about GC identifiers)

Start:	114,239,453 bp from pter	End:	114,302,111 bp from pter
Size:	62,659 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: PHTF1_HUMAN, Q9UMS5 (See protein sequence)

Recommended Name: Putative homeodomain transcription factor 1

Size: 762 amino acids; 87252 Da

Subunit: Interacts with FEM1B (By similarity)

Subcellular location: Nucleus (Potential)

Secondary accessions: Q5VWP7 Q5VWP8 Q9BUP2 Q9H1X8

Alternative splicing: 2 isoforms: Q9UMS5-1 Q9UMS5-2 (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PHTF1: NX_Q9UMS5

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9UMS5

PHTF1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_006599.2

ENSEMBL proteins:

ENSP00000358611 ENSP00000358613 ENSP00000358617 ENSP00000350428 ENSP00000416810

ENSP00000404690 ENSP00000377025 ENSP00000358609 ENSP00000393109

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	Uscn Proteins for PHTF1

Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005634	nucleus	IEA	--
GO:0005783	endoplasmic reticulum	--	--
GO:0005801	cis-Golgi network	--	--

PHTF1 for ontologies About GeneDecksing

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

PHTF1 for domains About GeneDecksing

1 InterPro domain/family:

IPR021980 TF_homeodomain_male

Graphical View of Domain Structure for InterPro Entry Q9UMS5

ProtoNet protein and cluster: Q9UMS5

1 Blocks protein family: IPB001092 Basic helix-loop-helix dimerization domain bHLH

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: PHTF1_HUMAN, Q9UMS5

Function: May play a role in transcription regulation

Genatlas biochemistry entry for PHTF1:

putative homeo domain transcription factor

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In Situ Assay
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Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003677	DNA binding	IEA	--
GO:0003700	sequence-specific DNA binding transcription factor activity	TAS	10729229

PHTF1 for ontologies About GeneDecksing

1 GenomeRNAi human phenotype for PHTF1:

Synthetic lethal with Ras

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for PHTF1

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

5/65 Interacting proteins for PHTF1 (Q9UMS5³ ENSP00000358617⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 65)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
HOXB9	P17482³, ENSP00000309439⁴	I2D: score=1 STRING: ENSP00000309439
CITED4	Q96RK1³	I2D: score=1
AGL	ENSP00000294724⁴	STRING: ENSP00000294724
AGMAT	ENSP00000364986⁴	STRING: ENSP00000364986
C10orf114	ENSP00000366317⁴	STRING: ENSP00000366317

About this table

Gene Ontology (GO): 2 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006351	transcription, DNA-dependent	IEA	--
GO:0006355	regulation of transcription, DNA-dependent	--	--

PHTF1 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for PHTF1
Search CenterWatch for drugs/clinical trials and news about PHTF1

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
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About This Section

REFSEQ mRNAs for PHTF1 gene:

NM_006608.2

Unigene Cluster for PHTF1:

Putative homeodomain transcription factor 1

Hs.655824 [show with all ESTs]

Unigene Representative Sequence: AK126773

14 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000474926(uc001edm.2) ENST00000369598 ENST00000369600 ENST00000369604

ENST00000481652 ENST00000357783(uc001edn.3) ENST00000412670(uc001edo.1)

ENST00000472612 ENST00000486855 ENST00000446739 ENST00000493212 ENST00000393357(uc009wgp.1)

ENST00000369596 ENST00000447664

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		hsa-miR-448 hsa-miR-4253 hsa-miR-3945 hsa-miR-548n
		SwitchGear 3'UTR luciferase reporter plasmid: PHTF1 3' UTR sequence

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Additional cDNA sequence:

AJ011863.1 AK126773.1 AK294749.1 BC000842.1 BC002447.2

13 DOTS entries:

DT.101971127 DT.92425584 DT.455123 DT.92425583 DT.121414101 DT.97782354 DT.411452 DT.456250

DT.40224258 DT.75157279 DT.95169064 DT.92425586 DT.91660829

24/95 AceView cDNA sequences (see all 95):

AW589714 BU634521 N64488 BQ229420 BM053136 CB107755 AA282015 AK126773

CB122664 AW517261 CK904013 AW771200 AW611842 CR606961 BP338402 BU170794

BQ223571 BM697670 BU176195 AI174526 BP368892 T84665 BC002447 AL600905

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

PHTF1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AAGCAAATAT

About this image

PHTF1 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

Posterior foregut-like cells (A scalable, suspensi...)

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See PHTF1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PHTF1

SOURCE GeneReport for Unigene cluster: Hs.655824

UniProtKB/Swiss-Prot: PHTF1_HUMAN, Q9UMS5

Tissue specificity: Widely expressed with highest levels in testis

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for PHTF1 gene from 5/18 species (see all 18) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Phtf1^{1 , 5}	putative homeodomain transcription factor 1^{1, 5}	90.1(n)¹ 93.69(a)¹		3 (45.52 cM)⁵ 18685¹ NM_001163467.1¹ NP_001156939.1¹ 103968110⁵
chicken (Gallus gallus)	Aves	PHTF1¹	putative homeodomain transcription factor 1	71.25(n) 74.9(a)		419878 XM_418005.3 XP_418005.3
lizard (Anolis carolinensis)	Reptilia	PHTF1⁶	--	72(a)	1 ↔ 1	4(139346118-139391290)
zebrafish (Danio rerio)	Actinopterygii	zgc:175264¹	zgc:175264	58.78(n) 58.28(a)		564764 NM_001114429.1 NP_001107901.1
fruit fly (Drosophila melanogaster)	Insecta	phtf³	--	41(a)		42C7 --

ENSEMBL Gene Tree for PHTF1 (if available)
TreeFam Gene Tree for PHTF1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for PHTF1 gene

PHTF2²

2 SIMAP similar genes for PHTF1 using alignment to 6 protein entries: PHTF1_HUMAN (see all proteins):

PHTF2 DKFZp564F013

PHTF1 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 1 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs147027808^1,2		--	114239329(+)	`AATGAG/TCAAGA`	1	--	ds500¹		0	--	--	--	--
rs11584572^1,2	C,F,H,	--	114239459(+)	`ACCTGA/GAAATG`	1	--	ds500¹		6		NS EA NA	540
rs138281759^1,2		--	114239464(+)	`AAAATA/GTACGG`	1	--	ds500¹		0	--	--	--	--
rs186664947^1,2		--	114239736(+)	`GTAAAC/TGAACA`	1	--	ds500¹		0	--	--	--	--
rs150918804^1,2		--	114240076(+)	`CCACA-/ACAC ACACA`	1	--	ut3¹		0	--	--	--	--
rs190664158^1,2		--	114240087(+)	`ACAGTC/GTTTAG`	1	--	ut3¹		0	--	--	--	--
rs182355676^1,2		--	114240124(+)	`AAGCAA/TGAAAA`	1	--	ut3¹		0	--	--	--	--
rs144286043^1,2		--	114240276(+)	`TCCTTC/GATAGG`	1	--	ut3¹		0	--	--	--	--
rs3835263^1,2	C,	--	114240319(-)	`TGAGT-/TAAATG`	1	--	ut3¹		0	--	--	--	--
rs113145080^1,2	C	--	114240319(+)	`GCATTA/TACTCA`	1	--	ut3¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for PHTF1 (114239453 - 114302111 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 4 variations for PHTF1
4 CNVs: 2322 3306 64644 43733

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

PHTF1 for disorders           About GeneDecksing

OMIM gene information: 604950    OMIM disorders: --

1 disease for PHTF1:    About MalaCards

asthma

Human Genome Epidemiology (HuGE) Navigator: PHTF1 (2 documents)

Export disorders for PHTF1 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for PHTF1 gene, integrated from 9 sources (see all 14):
(articles sorted by number of sources associating them with PHTF1)

Utopia: connect your pdf to the dynamic
world of online information

PHTF, a novel atypical homeobox gene on chromosome 1p13, is evolutionarily conserved. (PubMed id 10395808)^{1, 2, 3} Raich N.... Beaupain D. (1999)
The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)^{1, 2} Gregory S.G.... Bentley D.R. (2006)
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)
Molecular characterization of a novel gene family (PHTF) conserved from Drosophila to mammals. (PubMed id 10729229)^{1, 2} Manuel A.... Raich N. (2000)
Novel associations for hypothyroidism include known au toimmune risk loci. (PubMed id 22493691)¹ Eriksson N....Do C.B. (2012)
Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)¹ Rose J.E....Uhl G.R. (2010)
Allelic variants in the PHTF1-PTPN22, C12orf30 and CD 226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population. (PubMed id 20089178)¹ Douroudis K....Uibo R. (2010)
An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142)¹ Ravasi T....Hayashizaki Y. (2010)
PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes. (PubMed id 18305142)¹ Smyth D.J....Todd J.A. (2008)
Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. (PubMed id 17554260)¹ Todd J.A.... Clayton D.G. (2007)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		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: 10745	HGNC: 8939	AceView: PHTF1	Ensembl:ENSG00000116793	euGenes: HUgn10745
ECgene: PHTF1	H-InvDB: PHTF1

(According to HUGE)
About This Section

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

Name	Description
PharmGKB entry for PHTF1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for PHTF1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for PHTF1 gene:
Search GeneIP for patents involving PHTF1

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

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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About This Section


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GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes Disease genes PHTF1 gene at Home site.

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PHTF1 Gene

putative homeodomain transcription factor 1

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PHTF1 Gene

putative homeodomain transcription factor 1

Aliasesfor PHTF1 gene

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Genomic Viewsfor PHTF1 gene

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