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PHTF1 Gene

protein-coding   GIFtS: 53
GCID: GC01M114240

Putative Homeodomain Transcription Factor 1


(Previous symbol: PHTF)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for PHTF1 Gene:
PHTF1 (putative homeodomain transcription factor 1) is a protein-coding gene. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity. An important paralog of this gene is PHTF2.

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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NT_032977.10  NC_018912.2  
Regulatory elements:
   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 plasmidPHTF1 promoter sequence
   Search Chromatin IP Primers for PHTF1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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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)
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

Explore proteomics data for PHTF1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See PHTF1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_006599.2  
    ENSEMBL proteins: 
     ENSP00000358611   ENSP00000358613   ENSP00000358617   ENSP00000350428   ENSP00000416810  
     ENSP00000404690   ENSP00000377025   ENSP00000358609   ENSP00000393109  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR021980 TF_homeodomain_male

    Graphical View of Domain Structure for InterPro Entry Q9UMS5

    ProtoNet protein and cluster: Q9UMS5

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


    Find genes that share domains with PHTF1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PHTF1_HUMAN, Q9UMS5
    Function: May play a role in transcription regulation

         Genatlas biochemistry entry for PHTF1:
    putative homeo domain transcription factor

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity TAS10729229
         
    Find genes that share ontologies with PHTF1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for PHTF1:
     Synthetic lethal with Ras 

         1 MGI phenotypic allele for Phtf1 (no phenotypes)

    Find genes that share phenotypes with PHTF1           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for PHTF1

    miRNA
    Products:
        
    miRTarBase miRNAs that target PHTF1:
    hsa-mir-25-3p (MIRT050325), hsa-mir-484 (MIRT042377), hsa-mir-192-5p (MIRT026618), hsa-mir-21-5p (MIRT030876), hsa-mir-215-5p (MIRT024866), hsa-mir-615-3p (MIRT040056)

    Block miRNA regulation of human, mouse, rat PHTF1 using miScript Target Protectors
    4 qRT-PCR Assays for microRNAs that regulate PHTF1:
    hsa-miR-448 hsa-miR-4253 hsa-miR-3945 hsa-miR-548n
    SwitchGear 3'UTR luciferase reporter plasmidPHTF1 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PHTF1_HUMAN, Q9UMS5: Nucleus (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    plasma membrane3
    endoplasmic reticulum1
    golgi apparatus1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005783endoplasmic reticulum IEA--
    GO:0005801cis-Golgi network IEA--

    Find genes that share ontologies with PHTF1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PHTF1
    Interactions:

        Search GeneGlobe Interaction Network for PHTF1

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

    Selected Interacting proteins for PHTF1 (Q9UMS53 ENSP000003586174) via UniProtKB, MINT, STRING, and/or I2D (see all 65)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HOXB9P174823, ENSP000003094394I2D: score=1 STRING: ENSP00000309439
    CITED4Q96RK13I2D: score=1 
    GPX7ENSP000003546774STRING: ENSP00000354677
    PLOD1ENSP000001960614STRING: ENSP00000196061
    YBX1ENSP000003616264STRING: ENSP00000361626
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--

    Find genes that share ontologies with PHTF1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PHTF1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    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
    miRNA
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    4 qRT-PCR Assays for microRNAs that regulate PHTF1:
    hsa-miR-448 hsa-miR-4253 hsa-miR-3945 hsa-miR-548n
    SwitchGear 3'UTR luciferase reporter plasmidPHTF1 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat PHTF1
      QuantiFast Probe-based Assays in human, mouse, rat PHTF1

    Additional mRNA 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 

    Selected AceView cDNA sequences (see all 95):

    CB122664 BU176195 CR606961 BM053136 AW771200 AK126773 AA282015 BM697670 
    CB107755 BU634521 AW611842 BU170794 BQ229420 AW589714 BP338402 AI174526 
    AW517261 BQ223571 CK904013 N64488 AA649015 BE622903 AW235314 T84665 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PHTF1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAGCAAATAT
    PHTF1 Expression
    About this image

    PHTF1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PHTF1 Protein Expression

    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
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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)
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    This gene was present in the common ancestor of animals.

    Orthologs for PHTF1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Phtf11 , 5 putative homeodomain transcription factor 11, 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 70.71(n)
    74.7(a)
      419878  XM_004934998.1  XP_004935055.1 
    lizard
    (Anolis carolinensis)
    Reptilia PHTF16
    putative homeodomain transcription factor 1
    71(a)
    1 ↔ 1
    4(139345663-139391290)
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1752641 zgc:175264 58.94(n)
    57.61(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)
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    Paralogs for PHTF1 gene
    PHTF22  
    2 SIMAP similar genes for PHTF1 using alignment to 6 protein entries:     PHTF1_HUMAN (see all proteins):
    PHTF2    DKFZp564F013

    Find genes that share paralogs with PHTF1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PHTF1 (see all 1111)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs347993771,2
    C--112160955(+) GCTGC-/T/TTT 
            
    TTTTT
    1 -- us2k11NA 2
    rs1470278081,2
    --114239329(+) AATGAG/TCAAGA 1 -- ds50010--------
    rs115845721,2
    C,F,H--114239459(+) ACCTGA/GAAATG 1 -- ds50016Minor allele frequency- G:0.02NS EA NA 540
    rs1382817591,2
    C--114239464(+) AAAATA/GTACGG 1 -- ds50010--------
    rs1866649471,2
    --114239736(+) GTAAAC/TGAACA 1 -- ds50010--------
    rs1509188041,2
    C--114240076(+) CCACA-/ACAC  
            
    ACACA
    1 -- ut310--------
    rs1906641581,2
    --114240087(+) ACAGTC/GTTTAG 1 -- ut310--------
    rs1823556761,2
    --114240124(+) AAGCAA/TGAAAA 1 -- ut310--------
    rs1135641661,2
    C--114240150(+) TGCACG/ACCCAG 1 -- ut311Minor allele frequency- A:0.00CSA 1
    rs1442860431,2
    C--114240276(+) TCCTTC/GATAGG 1 -- ut310--------

    HapMap Linkage Disequilibrium report for PHTF1 (114239453 - 114302111 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for PHTF1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2179916CNV Deletion18987734
    esv23869CNV Loss19812545
    nsv831093CNV Loss17160897
    nsv872161CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
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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.)
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    OMIM gene information: 604950    OMIM disorders: --


    Find genes that share disorders with PHTF1           About GenesLikeMe

    Genetic Association Database (GAD): PHTF1
    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)
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    PubMed articles for PHTF1 gene, integrated from 10 sources (see all 16):
    (articles sorted by number of sources associating them with PHTF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. PHTF, a novel atypical homeobox gene on chromosome 1p13, is evolutionarily conserved. (PubMed id 10395808)1, 2, 3 Raich N.... Beaupain D. (Genomics 1999)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. 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, 4 Smyth D.J....Todd J.A. (Diabetes 2008)
    4. Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. (PubMed id 17554260)1, 4 Todd J.A.... Clayton D.G. (Nat. Genet. 2007)
    5. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    6. 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. (Genome Res. 2004)
    7. Molecular characterization of a novel gene family (PHTF) conserved from Drosophila to mammals. (PubMed id 10729229)1, 2 Manuel A.... Raich N. (Genomics 2000)
    8. Genetic variants associated with disordered eating. (PubMed id 23568457)1 Wade T.D....Martin N.G. (Int J Eat Disord 2013)
    9. Novel associations for hypothyroidism include known autoimmune risk loci. (PubMed id 22493691)1 Eriksson N....Do C.B. (PLoS ONE 2012)
    10. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    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)
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    Entrez Gene: 10745 HGNC: 8939 AceView: PHTF1 Ensembl:ENSG00000116793 euGenes: HUgn10745
    ECgene: PHTF1 H-InvDB: PHTF1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PHTF1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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