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

Gene ID: 324479, updated on 14-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
  • 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 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 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 
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 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
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