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    PHTF1 putative homeodomain transcription factor 1 [ Homo sapiens (human) ]

    Gene ID: 10745, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PHTF1provided by HGNC
    Official Full Name
    putative homeodomain transcription factor 1provided by HGNC
    Primary source
    HGNC:HGNC:8939
    See related
    Ensembl:ENSG00000116793 MIM:604950; AllianceGenome:HGNC:8939
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PHTF
    Summary
    Predicted to be located in cis-Golgi network membrane and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 15.3), gall bladder (RPKM 3.5) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHTF1 in Genome Data Viewer
    Location:
    1p13.2
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (113696831..113759888, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (113708467..113771550, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114239453..114302510, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene membrane associated guanylate kinase, WW and PDZ domain containing 3 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene Neighboring gene Sharpr-MPRA regulatory region 10793 Neighboring gene MT-ND5 pseudogene 20 Neighboring gene NANOG hESC enhancer GRCh37_chr1:114181286-114181787 Neighboring gene Sharpr-MPRA regulatory region 12988 Neighboring gene NANOG hESC enhancer GRCh37_chr1:114223507-114224045 Neighboring gene ribosomal protein S2 pseudogene 14 Neighboring gene Sharpr-MPRA regulatory region 5734 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:114295082-114295283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114299147-114299702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1215 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:114301981-114302560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1216 Neighboring gene Sharpr-MPRA regulatory region 4295 Neighboring gene round spermatid basic protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:114353909-114354438 Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chr1:114354439-114354968 and GRCh37_chr1:114354969-114355498 Neighboring gene AP4B1 antisense RNA 1 Neighboring gene protein tyrosine phosphatase non-receptor type 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1538

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Life after log. Siegele DA, et al. J Bacteriol, 1992 Jan. PMID 1729229, Free PMC Article
    2. PHTF, a novel atypical homeobox gene on chromosome 1p13, is evolutionarily conserved. Raich N, et al. Genomics, 1999 Jul 1. PMID 10395808
    3. PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes. Smyth DJ, et al. Diabetes, 2008 Jun. PMID 18305142
    4. Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population. Douroudis K, et al. BMC Med Genet, 2010 Jan 20. PMID 20089178, Free PMC Article
    5. Molecular characterization of a novel gene family (PHTF) conserved from Drosophila to mammals. Manuel A, et al. Genomics, 2000 Mar 1. PMID 10729229

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    2. Results supports the rs6679677 (PHTF1-PTPN22) SNP as a susceptibility factor for type 1 diabetes.
      Title: Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
    EBI GWAS Catalog
    Genetic variants associated with disordered eating.
    EBI GWAS Catalog
    Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
    EBI GWAS Catalog
    Novel associations for hypothyroidism include known autoimmune risk loci.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in cis-Golgi network membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein PHTF1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001323041.2 → NP_001309970.1  protein PHTF1 isoform a

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321
      Consensus CDS
      CCDS861.1
      UniProtKB/Swiss-Prot
      Q5VWP7, Q5VWP8, Q9BUP2, Q9H1X8, Q9UMS5
      UniProtKB/TrEMBL
      Q5TCQ5
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    2. NM_001323042.2 → NP_001309971.1  protein PHTF1 isoform a

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321
      Consensus CDS
      CCDS861.1
      UniProtKB/Swiss-Prot
      Q5VWP7, Q5VWP8, Q9BUP2, Q9H1X8, Q9UMS5
      UniProtKB/TrEMBL
      Q5TCQ5
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    3. NM_001323043.2 → NP_001309972.1  protein PHTF1 isoform a

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321
      Consensus CDS
      CCDS861.1
      UniProtKB/Swiss-Prot
      Q5VWP7, Q5VWP8, Q9BUP2, Q9H1X8, Q9UMS5
      UniProtKB/TrEMBL
      Q5TCQ5
      Related
      ENSP00000358617.1, ENST00000369604.6
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    4. NM_001323044.2 → NP_001309973.1  protein PHTF1 isoform b

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321
      UniProtKB/TrEMBL
      Q5TCQ5
      Conserved Domains (1) summary
      pfam12129
      Location:1 → 107
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    5. NM_001323045.2 → NP_001309974.1  protein PHTF1 isoform b

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321
      UniProtKB/TrEMBL
      Q5TCQ5
      Conserved Domains (1) summary
      pfam12129
      Location:1 → 107
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    6. NM_001323046.2 → NP_001309975.1  protein PHTF1 isoform c

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321

    7. NM_001323047.2 → NP_001309976.1  protein PHTF1 isoform d

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321
      Consensus CDS
      CCDS81359.1
      UniProtKB/TrEMBL
      Q5TCQ5
      Related
      ENSP00000350428.2, ENST00000357783.6
      Conserved Domains (1) summary
      pfam12129
      Location:6 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    8. NM_001323048.2 → NP_001309977.1  protein PHTF1 isoform d

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321
      Consensus CDS
      CCDS81359.1
      UniProtKB/TrEMBL
      Q5TCQ5
      Conserved Domains (1) summary
      pfam12129
      Location:6 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    9. NM_001323049.2 → NP_001309978.1  protein PHTF1 isoform d

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321
      Consensus CDS
      CCDS81359.1
      UniProtKB/TrEMBL
      Q5TCQ5
      Conserved Domains (1) summary
      pfam12129
      Location:6 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    10. NM_001323050.2 → NP_001309979.1  protein PHTF1 isoform e

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321

    11. NM_001323051.2 → NP_001309980.1  protein PHTF1 isoform f

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321

    12. NM_001323052.2 → NP_001309981.1  protein PHTF1 isoform g

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    13. NM_001323053.2 → NP_001309982.1  protein PHTF1 isoform g

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    14. NM_006608.3 → NP_006599.2  protein PHTF1 isoform a

      See identical proteins and their annotated locations for NP_006599.2

      Status: VALIDATED

      Source sequence(s)
      AJ011863, AK126773, AL133517, AL365321, BC002447, CX763183, DA728266, DB457884
      Consensus CDS
      CCDS861.1
      UniProtKB/Swiss-Prot
      Q5VWP7, Q5VWP8, Q9BUP2, Q9H1X8, Q9UMS5
      UniProtKB/TrEMBL
      Q5TCQ5
      Related
      ENSP00000377025.2, ENST00000393357.6
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    RNA

    1. NR_136564.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321

    2. NR_136565.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321

    3. NR_136566.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321

    4. NR_136567.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321

    5. NR_136568.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL133517, AL365321

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      113696831..113759888 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      113708467..113771550 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UMS5.2 GenPept UniProtKB/Swiss-Prot:Q9UMS5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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