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    PHTF2 putative homeodomain transcription factor 2 [ Homo sapiens (human) ]

    Gene ID: 57157, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PHTF2provided by HGNC
    Official Full Name
    putative homeodomain transcription factor 2provided by HGNC
    Primary source
    HGNC:HGNC:13411
    See related
    Ensembl:ENSG00000006576 MIM:616785; AllianceGenome:HGNC:13411
    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
    Summary
    Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 6.3), appendix (RPKM 5.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHTF2 in Genome Data Viewer
    Location:
    7q11.23-q21.11
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (77798773..77957504)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (79050700..79209413)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (77428090..77586821)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:77324871-77325766 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:77325767-77326662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77393580-77394080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26209 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:77464234-77464734 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18331 Neighboring gene round spermatid basic protein 1 like Neighboring gene Alu-mediated CDKN1A/p21 transcriptional regulator Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:77501601-77502172 Neighboring gene uncharacterized LOC124901682 Neighboring gene transmembrane protein 60 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:77619182-77620381 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:77635196-77635696 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:77648359-77648860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18332 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77677051-77677551 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:77703601-77704220 Neighboring gene DDX3 interacting lncRNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77763787-77764288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77764289-77764788 Neighboring gene uncharacterized LOC124901684 Neighboring gene membrane associated guanylate kinase, WW and PDZ domain containing 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Molecular characterization of a novel gene family (PHTF) conserved from Drosophila to mammals. Manuel A, et al. Genomics, 2000 Mar 1. PMID 10729229
    2. GWAS of dental caries patterns in the permanent dentition. Shaffer JR, et al. J Dent Res, 2013 Jan. PMID 23064961, Free PMC Article
    3. New loci associated with kidney function and chronic kidney disease. Köttgen A, et al. Nat Genet, 2010 May. PMID 20383146, Free PMC Article
    4. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. Simpson JC, et al. EMBO Rep, 2000 Sep. PMID 11256614, Free PMC Article
    5. The LIFEdb database in 2006. Mehrle A, et al. Nucleic Acids Res, 2006 Jan 1. PMID 16381901, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    GWAS of dental caries patterns in the permanent dentition.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    Clone Names

    • FLJ33324, MGC86999, DKFZp564F013

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein PHTF2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001127357.2 → NP_001120829.1  protein PHTF2 isoform 1

      See identical proteins and their annotated locations for NP_001120829.1

      Status: VALIDATED

      Source sequence(s)
      AC073520, AL136883, BC022419, BC127093, CB051673
      Consensus CDS
      CCDS47621.1
      UniProtKB/Swiss-Prot
      Q8N3S3
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 158
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    2. NM_001127358.2 → NP_001120830.1  protein PHTF2 isoform 2

      See identical proteins and their annotated locations for NP_001120830.1

      Status: VALIDATED

      Source sequence(s)
      AC004955, AK225854, AL136883, BP321440, CB051673
      Consensus CDS
      CCDS47622.1
      UniProtKB/Swiss-Prot
      Q8N3S3
      Related
      ENSP00000307699.8, ENST00000307305.12
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    3. NM_001127359.2 → NP_001120831.1  protein PHTF2 isoform 3

      See identical proteins and their annotated locations for NP_001120831.1

      Status: VALIDATED

      Source sequence(s)
      AC004990, AC073520, BC022419, BE880432, BP395569
      Consensus CDS
      CCDS47623.1
      UniProtKB/Swiss-Prot
      Q8N3S3
      Related
      ENSP00000387355.1, ENST00000450574.5
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 156
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    4. NM_001127360.2 → NP_001120832.1  protein PHTF2 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, BC022419, BC067742, BE880432, BP321440, BP395569
      Consensus CDS
      CCDS47624.1
      UniProtKB/Swiss-Prot
      Q8N3S3
      Related
      ENSP00000408035.2, ENST00000415251.6
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    5. NM_001366081.1 → NP_001353010.1  protein PHTF2 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, AL136883
      Consensus CDS
      CCDS94133.1
      Related
      ENSP00000275575.7, ENST00000275575.11
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    6. NM_001366082.2 → NP_001353011.1  protein PHTF2 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC004955, AK090643, BQ014377
      Consensus CDS
      CCDS94134.1
      Related
      ENSP00000403620.1, ENST00000424760.5
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    7. NM_001366083.1 → NP_001353012.1  protein PHTF2 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, AC073520
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    8. NM_001366084.1 → NP_001353013.1  protein PHTF2 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, AC073520
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    9. NM_001366085.2 → NP_001353014.1  protein PHTF2 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, AC073520
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    10. NM_001366086.1 → NP_001353015.1  protein PHTF2 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, AC073520
      Consensus CDS
      CCDS47622.1
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    11. NM_001366087.1 → NP_001353016.1  protein PHTF2 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, AC073520
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    12. NM_001366088.2 → NP_001353017.1  protein PHTF2 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, AC073520
      Consensus CDS
      CCDS94134.1
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    13. NM_001366089.1 → NP_001353018.1  protein PHTF2 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC004990, AC073520
      Consensus CDS
      CCDS94132.1
      UniProtKB/Swiss-Prot
      A0JP04, A0JP05, A4D1C2, B3KQZ2, E9PEE3, G5E9H7, Q6NW35, Q8N3S3, Q8TBW4, Q9H099
      Related
      ENSP00000248550.7, ENST00000248550.7
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 190
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    14. NM_001395270.1 → NP_001382199.1  protein PHTF2 isoform 11

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, AC073520
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 154
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    15. NM_001395271.1 → NP_001382200.1  protein PHTF2 isoform 12

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, AC073520
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 158
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    16. NM_001395272.1 → NP_001382201.1  protein PHTF2 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC004955, AC004990, AC073520
      Consensus CDS
      CCDS47621.1
      Related
      ENSP00000403042.2, ENST00000422959.8
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 158
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    17. NM_020432.5 → NP_065165.3  protein PHTF2 isoform 2

      See identical proteins and their annotated locations for NP_065165.3

      Status: VALIDATED

      Source sequence(s)
      AC073520, AL136883, BC022419, BC127094, CB051673
      Consensus CDS
      CCDS47622.1
      UniProtKB/Swiss-Prot
      Q8N3S3
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 152
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      77798773..77957504
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011516422.4 → XP_011514724.1  protein PHTF2 isoform X2

      Conserved Domains (1) summary
      pfam12129
      Location:5 → 156
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    2. XM_011516423.4 → XP_011514725.1  protein PHTF2 isoform X4

      Conserved Domains (1) summary
      pfam12129
      Location:5 → 156
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    3. XM_047420638.1 → XP_047276594.1  protein PHTF2 isoform X3

    4. XM_047420640.1 → XP_047276596.1  protein PHTF2 isoform X5

    5. XM_005250509.5 → XP_005250566.1  protein PHTF2 isoform X1

      See identical proteins and their annotated locations for XP_005250566.1

      UniProtKB/Swiss-Prot
      Q8N3S3
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 158
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    6. XM_047420639.1 → XP_047276595.1  protein PHTF2 isoform X3

    7. XM_011516424.3 → XP_011514726.1  protein PHTF2 isoform X6

      Conserved Domains (1) summary
      pfam12129
      Location:1 → 15
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      79050700..79209413
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358687.1 → XP_054214662.1  protein PHTF2 isoform X2

    2. XM_054358690.1 → XP_054214665.1  protein PHTF2 isoform X4

    3. XM_054358688.1 → XP_054214663.1  protein PHTF2 isoform X3

    4. XM_054358691.1 → XP_054214666.1  protein PHTF2 isoform X5

    5. XM_054358686.1 → XP_054214661.1  protein PHTF2 isoform X1

    6. XM_054358689.1 → XP_054214664.1  protein PHTF2 isoform X3

    7. XM_054358692.1 → XP_054214667.1  protein PHTF2 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N3S3.2 GenPept UniProtKB/Swiss-Prot:Q8N3S3

    Gene LinkOut

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