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    bptf bromodomain PHD finger transcription factor [ Danio rerio (zebrafish) ]

    Gene ID: 324479, updated on 2-Nov-2024

    Summary

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    Official Symbol
    bptfprovided by ZNC
    Official Full Name
    bromodomain PHD finger transcription factorprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-3200
    See related
    Ensembl:ENSDARG00000077361 AllianceGenome:ZFIN:ZDB-GENE-030131-3200
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fc30e02; fc32a05; wu:fb71f11; wu:fc30e02; wu:fc32a05
    Summary
    Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and histone octamer slider activity. Acts upstream of or within cranial skeletal system development; neural plate anterior/posterior regionalization; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of NURF complex. Is expressed in head and hematopoietic multipotent progenitor cell. Human ortholog(s) of this gene implicated in Kaposi's sarcoma; alcohol dependence; and neurodevelopmental disorder with dysmorphic facies and distal limb anomalies. Orthologous to human BPTF (bromodomain PHD finger transcription factor). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See bptf in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (25379152..25421160, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (25248337..25290861, complement)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene SMAD specific E3 ubiquitin protein ligase 2 Neighboring gene karyopherin alpha 2 (RAG cohort 1, importin alpha 1) Neighboring gene transfer RNA serine (anticodon AGA) Neighboring gene growth factor receptor-bound protein 2b

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Haploinsufficiency of the Chromatin Remodeler BPTF Causes Syndromic Developmental and Speech Delay, Postnatal Microcephaly, and Dysmorphic Features. Stankiewicz P, et al. Am J Hum Genet, 2017 Oct 5. PMID 28942966, Free PMC Article
    2. The Chromatin Remodeling Protein Bptf Promotes Posterior Neuroectodermal Fate by Enhancing Smad2-Activated wnt8a Expression. Ma Y, et al. J Neurosci, 2015 Jun 3. PMID 26041917, Free PMC Article
    3. Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates. Ding Y, et al. Blood, 2021 Jan 14. PMID 32756943, Free PMC Article
    4. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
    5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The results of this study found that Bptf and TGF-beta/Smad2 mediate nucleosome remodeling to regulate wnt8a expression and hence neural posteriorization.
      Title: The Chromatin Remodeling Protein Bptf Promotes Posterior Neuroectodermal Fate by Enhancing Smad2-Activated wnt8a Expression.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone octamer slider activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methylated histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cranial skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within neural plate anterior/posterior regionalization IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within neural plate anterior/posterior regionalization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of NURF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of NURF complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    nucleosome-remodeling factor subunit BPTF

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007114.7 Reference GRCz11 Primary Assembly

      Range
      25379152..25421160 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068218967.1 → XP_068075068.1  nucleosome-remodeling factor subunit BPTF isoform X8

    2. XM_068218965.1 → XP_068075066.1  nucleosome-remodeling factor subunit BPTF isoform X6

    3. XM_009299418.4 → XP_009297693.1  nucleosome-remodeling factor subunit BPTF isoform X2

      UniProtKB/TrEMBL
      A0A8M3B894, E7F366
      Related
      ENSDARP00000102656.5, ENSDART00000109601.5
      Conserved Domains (7) summary
      cd05509
      Location:2784 → 2884
      Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...
      cd15559
      Location:348 → 390
      PHD1_BPTF; PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      cd15560
      Location:2722 → 2768
      PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      pfam02791
      Location:197 → 253
      DDT; DDT domain
      pfam10252
      Location:1832 → 1880
      PP28; Casein kinase substrate phosphoprotein PP28
      pfam15612
      Location:295 → 344
      WHIM1; WSTF, HB1, Itc1p, MBD9 motif 1
      pfam15613
      Location:413 → 438
      WHIM2; WSTF, HB1, Itc1p, MBD9 motif 2

    4. XM_068218966.1 → XP_068075067.1  nucleosome-remodeling factor subunit BPTF isoform X7

    5. XM_068218975.1 → XP_068075076.1  nucleosome-remodeling factor subunit BPTF isoform X12

    6. XM_005171627.5 → XP_005171684.1  nucleosome-remodeling factor subunit BPTF isoform X5

      UniProtKB/TrEMBL
      A0A8M2BJ03
      Conserved Domains (7) summary
      cd05509
      Location:2770 → 2870
      Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...
      cd15559
      Location:349 → 391
      PHD1_BPTF; PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      cd15560
      Location:2708 → 2754
      PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      pfam02791
      Location:198 → 254
      DDT; DDT domain
      pfam10252
      Location:1818 → 1866
      PP28; Casein kinase substrate phosphoprotein PP28
      pfam15612
      Location:296 → 345
      WHIM1; WSTF, HB1, Itc1p, MBD9 motif 1
      pfam15613
      Location:414 → 439
      WHIM2; WSTF, HB1, Itc1p, MBD9 motif 2

    7. XM_009299419.4 → XP_009297694.1  nucleosome-remodeling factor subunit BPTF isoform X3

      UniProtKB/TrEMBL
      A0A8M3AQV1
      Conserved Domains (7) summary
      cd05509
      Location:2784 → 2884
      Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...
      cd15559
      Location:349 → 391
      PHD1_BPTF; PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      cd15560
      Location:2722 → 2768
      PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      pfam02791
      Location:198 → 254
      DDT; DDT domain
      pfam10252
      Location:1832 → 1880
      PP28; Casein kinase substrate phosphoprotein PP28
      pfam15612
      Location:296 → 345
      WHIM1; WSTF, HB1, Itc1p, MBD9 motif 1
      pfam15613
      Location:414 → 439
      WHIM2; WSTF, HB1, Itc1p, MBD9 motif 2

    8. XM_017354770.3 → XP_017210259.1  nucleosome-remodeling factor subunit BPTF isoform X13

      UniProtKB/TrEMBL
      A0A8M6YWR8
      Related
      ENSDARP00000147173.1, ENSDART00000182184.1

    9. XM_068218976.1 → XP_068075077.1  nucleosome-remodeling factor subunit BPTF isoform X14

      Related
      ENSDARP00000128418.1, ENSDART00000154200.3

    10. XM_009299421.4 → XP_009297696.1  nucleosome-remodeling factor subunit BPTF isoform X9

      UniProtKB/TrEMBL
      A0A8M3AXZ5
      Conserved Domains (7) summary
      cd05509
      Location:2758 → 2858
      Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...
      cd15559
      Location:349 → 391
      PHD1_BPTF; PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      cd15560
      Location:2696 → 2742
      PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      pfam02791
      Location:198 → 254
      DDT; DDT domain
      pfam14282
      Location:2401 → 2462
      FlxA; FlxA-like protein
      pfam15612
      Location:296 → 345
      WHIM1; WSTF, HB1, Itc1p, MBD9 motif 1
      pfam15613
      Location:414 → 439
      WHIM2; WSTF, HB1, Itc1p, MBD9 motif 2

    11. XM_017354769.3 → XP_017210258.1  nucleosome-remodeling factor subunit BPTF isoform X10

      UniProtKB/TrEMBL
      A0A8M6Z5Q1

    12. XM_068218972.1 → XP_068075073.1  nucleosome-remodeling factor subunit BPTF isoform X11

    13. XM_009299417.4 → XP_009297692.1  nucleosome-remodeling factor subunit BPTF isoform X1

      UniProtKB/TrEMBL
      A0A8M3AQI5
      Conserved Domains (7) summary
      cd05509
      Location:2785 → 2885
      Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...
      cd15559
      Location:349 → 391
      PHD1_BPTF; PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      cd15560
      Location:2723 → 2769
      PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      pfam02791
      Location:198 → 254
      DDT; DDT domain
      pfam10252
      Location:1833 → 1881
      PP28; Casein kinase substrate phosphoprotein PP28
      pfam15612
      Location:296 → 345
      WHIM1; WSTF, HB1, Itc1p, MBD9 motif 1
      pfam15613
      Location:414 → 439
      WHIM2; WSTF, HB1, Itc1p, MBD9 motif 2

    14. XM_009299420.4 → XP_009297695.1  nucleosome-remodeling factor subunit BPTF isoform X4

      UniProtKB/TrEMBL
      A0A8M3B0X4
      Conserved Domains (7) summary
      cd05509
      Location:2785 → 2885
      Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...
      cd15559
      Location:349 → 391
      PHD1_BPTF; PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      cd15560
      Location:2723 → 2769
      PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)
      pfam02791
      Location:198 → 254
      DDT; DDT domain
      pfam10252
      Location:1833 → 1881
      PP28; Casein kinase substrate phosphoprotein PP28
      pfam15612
      Location:296 → 345
      WHIM1; WSTF, HB1, Itc1p, MBD9 motif 1
      pfam15613
      Location:414 → 439
      WHIM2; WSTF, HB1, Itc1p, MBD9 motif 2
    Nucleotide Protein Strain
    Heading Accession and Version

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