Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PHTF1 Gene

Aliases for PHTF1 Gene

  • Putative Homeodomain Transcription Factor 1 2 3 5
  • PHTF 3 4

External Ids for PHTF1 Gene

Previous HGNC Symbols for PHTF1 Gene

  • PHTF

Previous GeneCards Identifiers for PHTF1 Gene

  • GC01M114653
  • GC01M113122
  • GC01M113339
  • GC01M113538
  • GC01M113951
  • GC01M114240
  • GC01M112097

Summaries for PHTF1 Gene

GeneCards Summary for PHTF1 Gene

PHTF1 (Putative Homeodomain Transcription Factor 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity. An important paralog of this gene is PHTF2.

UniProtKB/Swiss-Prot for PHTF1 Gene

  • May play a role in transcription regulation.

Additional gene information for PHTF1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHTF1 Gene

Genomics for PHTF1 Gene

GeneHancer (GH) Regulatory Elements for PHTF1 Gene

Promoters and enhancers for PHTF1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I113757 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 559.7 +0.8 824 3.6 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 PHTF1 LOC100421402 RSBN1 TRIM33 LRIG2 AP4B1 AP4B1-AS1 RPS2P14
GH01I113869 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 17.8 -113.3 -113287 7.6 HDGF PKNOX1 ATF1 SMAD1 YBX1 IRF4 ZNF766 ZNF207 ZNF143 ATF7 PTPN22 AP4B1 PHTF1 RSBN1 DCLRE1B ENSG00000231128 HIPK1 HIPK1-AS1 OLFML3 AP4B1-AS1
GH01I113809 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.1 -51.7 -51660 4.7 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC ZNF610 NBN NR2C1 RSBN1 AP4B1-AS1 ENSG00000231128 LOC100421402 TRIM33 LRIG2 SIKE1 PHTF1 OLFML3 AP4B1
GH01I113779 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 14.4 -23.3 -23296 6.4 HDGF ATF1 PKNOX1 CLOCK SMAD1 FEZF1 TCF12 ATF7 RUNX3 JUNB RSBN1 PHTF1 ENSG00000231128 AP4B1 MAGI3 PTPN22 HIPK1 PIR59903
GH01I113878 Enhancer 0.9 Ensembl ENCODE 16.5 -120.5 -120543 3.2 HDGF PAX8 NFXL1 ZBTB40 ZNF664 ATF7 IKZF2 BCLAF1 RUNX3 ZNF687 AP4B1 PHTF1 DCLRE1B HIPK1-AS1 HIPK1 OLFML3 MAGI3 BCL2L15 PTPN22 AP4B1-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHTF1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHTF1 gene promoter:

Genomic Locations for PHTF1 Gene

Genomic Locations for PHTF1 Gene
63,062 bases
Minus strand

Genomic View for PHTF1 Gene

Genes around PHTF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHTF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHTF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHTF1 Gene

Proteins for PHTF1 Gene

  • Protein details for PHTF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Putative homeodomain transcription factor 1
    Protein Accession:
    Secondary Accessions:
    • Q5VWP7
    • Q5VWP8
    • Q9BUP2
    • Q9H1X8

    Protein attributes for PHTF1 Gene

    762 amino acids
    Molecular mass:
    87252 Da
    Quaternary structure:
    • Interacts with FEM1B.

    Alternative splice isoforms for PHTF1 Gene


neXtProt entry for PHTF1 Gene

Post-translational modifications for PHTF1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for PHTF1 Gene

Domains & Families for PHTF1 Gene

Gene Families for PHTF1 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted membrane proteins
  • Transcription factors

Protein Domains for PHTF1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PHTF1: view

No data available for UniProtKB/Swiss-Prot for PHTF1 Gene

Function for PHTF1 Gene

Molecular function for PHTF1 Gene

GENATLAS Biochemistry:
putative homeo domain transcription factor
UniProtKB/Swiss-Prot Function:
May play a role in transcription regulation.

Phenotypes From GWAS Catalog for PHTF1 Gene

Gene Ontology (GO) - Molecular Function for PHTF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity TAS 10729229
genes like me logo Genes that share ontologies with PHTF1: view
genes like me logo Genes that share phenotypes with PHTF1: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PHTF1 Gene

Localization for PHTF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHTF1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHTF1 gene
Compartment Confidence
nucleus 4
plasma membrane 3
endoplasmic reticulum 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PHTF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005801 cis-Golgi network IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PHTF1: view

Pathways & Interactions for PHTF1 Gene

SuperPathways for PHTF1 Gene

No Data Available

Interacting Proteins for PHTF1 Gene

Selected Interacting proteins: Q9UMS5-PHTF1_HUMAN for PHTF1 Gene via IID

Gene Ontology (GO) - Biological Process for PHTF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with PHTF1: view

No data available for Pathways by source and SIGNOR curated interactions for PHTF1 Gene

Drugs & Compounds for PHTF1 Gene

No Compound Related Data Available

Transcripts for PHTF1 Gene

Unigene Clusters for PHTF1 Gene

Putative homeodomain transcription factor 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHTF1 Gene

No ASD Table

Relevant External Links for PHTF1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PHTF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHTF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PHTF1 Gene

This gene is overexpressed in Brain - Cerebellum (x4.6) and Brain - Cerebellar Hemisphere (x4.6).

Protein differential expression in normal tissues from HIPED for PHTF1 Gene

This gene is overexpressed in Serum (57.7) and Plasma (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PHTF1 Gene

Protein tissue co-expression partners for PHTF1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PHTF1 Gene:


SOURCE GeneReport for Unigene cluster for PHTF1 Gene:


mRNA Expression by UniProt/SwissProt for PHTF1 Gene:

Tissue specificity: Widely expressed with highest levels in testis.

Evidence on tissue expression from TISSUES for PHTF1 Gene

  • Skin(4.1)
genes like me logo Genes that share expression patterns with PHTF1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PHTF1 Gene

Orthologs for PHTF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PHTF1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PHTF1 33 34
  • 99.83 (n)
(Canis familiaris)
Mammalia PHTF1 33 34
  • 93.39 (n)
(Bos Taurus)
Mammalia PHTF1 33 34
  • 91.95 (n)
(Mus musculus)
Mammalia Phtf1 33 16 34
  • 90.1 (n)
(Rattus norvegicus)
Mammalia Phtf1 33
  • 90.03 (n)
(Monodelphis domestica)
Mammalia PHTF1 34
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia PHTF1 34
  • 79 (a)
(Gallus gallus)
Aves PHTF1 33 34
  • 70.71 (n)
(Anolis carolinensis)
Reptilia PHTF1 34
  • 71 (a)
(Danio rerio)
Actinopterygii zgc:175264 33
  • 58.94 (n)
PHTF1 34
  • 55 (a)
fruit fly
(Drosophila melanogaster)
Insecta phtf 35 34
  • 41 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 58 (a)
Species where no ortholog for PHTF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PHTF1 Gene

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

Paralogs for PHTF1 Gene

Paralogs for PHTF1 Gene

(2) SIMAP similar genes for PHTF1 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with PHTF1: view

Variants for PHTF1 Gene

Sequence variations from dbSNP and Humsavar for PHTF1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000135258 -- 113,757,897(-) A/G intron_variant
rs1000197231 -- 113,723,236(-) G/A intron_variant
rs1000229929 -- 113,716,716(-) T/A intron_variant
rs1000236832 -- 113,702,065(-) C/G genic_downstream_transcript_variant, intron_variant
rs1000242644 -- 113,750,720(-) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PHTF1 Gene

Variant ID Type Subtype PubMed ID
nsv831093 CNV loss 17160897
esv3587246 CNV loss 21293372
esv3587245 CNV loss 21293372
esv3587240 CNV loss 21293372
esv3587239 CNV loss 21293372
esv23869 CNV loss 19812545
esv2179916 CNV deletion 18987734

Variation tolerance for PHTF1 Gene

Residual Variation Intolerance Score: 32.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.30; 41.09% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHTF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHTF1 Gene

Disorders for PHTF1 Gene

Additional Disease Information for PHTF1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PHTF1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PHTF1 Gene

Publications for PHTF1 Gene

  1. PHTF, a novel atypical homeobox gene on chromosome 1p13, is evolutionarily conserved. (PMID: 10395808) Raich N … Beaupain D (Genomics 1999) 2 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes. (PMID: 18305142) Smyth DJ … Todd JA (Diabetes 2008) 3 44 58
  4. Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. (PMID: 17554260) Todd JA … Clayton DG (Nature genetics 2007) 3 44 58
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58

Products for PHTF1 Gene

Sources for PHTF1 Gene

Loading form....