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    DPF1 double PHD fingers 1 [ Homo sapiens (human) ]

    Gene ID: 8193, updated on 14-Nov-2024

    Summary

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    Official Symbol
    DPF1provided by HGNC
    Official Full Name
    double PHD fingers 1provided by HGNC
    Primary source
    HGNC:HGNC:20225
    See related
    Ensembl:ENSG00000011332 MIM:601670; AllianceGenome:HGNC:20225
    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
    NEUD4; BAF45b; SMARCG1; neuro-d4
    Summary
    Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in nervous system development. Predicted to be located in nucleoplasm. Predicted to be part of nBAF complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in brain (RPKM 6.5) and testis (RPKM 0.6) See more
    Orthologs
    mouse all
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    Genomic context

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    See DPF1 in Genome Data Viewer
    Location:
    19q13.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (38211006..38229695, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (41013164..41031861, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (38701646..38720335, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene signal induced proliferation associated 1 like 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38656938-38657140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38661080-38661641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38666131-38666631 Neighboring gene small nucleolar RNA, C/D box 152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38693513-38694196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38700253-38701236 Neighboring gene RNA, 7SL, cytoplasmic 663, pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:38707788-38708987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38709595-38710094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10563 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38718119-38718889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14569 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38729145-38729644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38734884-38735760 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38746806-38746993 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38751829-38752766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38752767-38753703 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38753844-38754761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10565 Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 14A Neighboring gene serine peptidase inhibitor, Kunitz type 2

    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 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. BAF45b Is Required for Efficient Zika Virus Infection of HAP1 Cells. Persson BD, et al. Viruses, 2021 Oct 6. PMID 34696437, Free PMC Article
    2. The d4 gene family in the human genome. Chestkov AV, et al. Genomics, 1996 Aug 15. PMID 8812431
    3. Double plant homeodomain (PHD) finger proteins DPF3a and -3b are required as transcriptional co-activators in SWI/SNF complex-dependent activation of NF-κB RelA/p50 heterodimer. Ishizaka A, et al. J Biol Chem, 2012 Apr 6. PMID 22334708, Free PMC Article
    4. Regulation of dendritic development by neuron-specific chromatin remodeling complexes. Wu JI, et al. Neuron, 2007 Oct 4. PMID 17920018
    5. Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate male germline transcription in the mouse. Menon DU, et al. Development, 2019 Jul 5. PMID 31043422, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. BAF45b Is Required for Efficient Zika Virus Infection of HAP1 Cells.
      Title: BAF45b Is Required for Efficient Zika Virus Infection of HAP1 Cells.
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC150428, MGC150429

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nervous system development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of cell differentiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of double-strand break repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of G0 to G1 transition NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of G1/S transition of mitotic cell cycle NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of mitotic metaphase/anaphase transition NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of nucleotide-excision repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of nBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of nBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of nBAF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein neuro-d4
    Names
    BRG1-associated factor 45B
    D4, zinc and double PHD fingers family 1
    neuro-d4 homolog

    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_001135155.3 → NP_001128627.2  zinc finger protein neuro-d4 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) uses an alternate in-frame splice site in the 3' coding region, compared to variant 4. The encoded protein (isoform a) is shorter, compared to isoform d.
      Source sequence(s)
      AC011479, BC125153
      Consensus CDS
      CCDS46064.2
      UniProtKB/Swiss-Prot
      B3KSY8, Q08AJ0, Q92782
      UniProtKB/TrEMBL
      A0A804CCM0, Q6PJ73
      Related
      ENSP00000347716.5, ENST00000355526.10
      Conserved Domains (4) summary
      COG5189
      Location:185 → 219
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:327 → 372
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:269 → 326
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:12 → 78
      Requiem_N; N-terminal domain of DPF2/REQ

    2. NM_001135156.3 → NP_001128628.1  zinc finger protein neuro-d4 isoform c

      See identical proteins and their annotated locations for NP_001128628.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple coding region differences, including use of a downstream translation initiation codon, compared to variant 4. The encoded protein (isoform c) is shorter than isoform d.
      Source sequence(s)
      AC011479, AI885717, AK094632, AL538568, BC021191
      Consensus CDS
      CCDS46065.1
      UniProtKB/TrEMBL
      Q6PJ73
      Related
      ENSP00000412098.1, ENST00000412732.5
      Conserved Domains (4) summary
      COG5189
      Location:130 → 164
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:272 → 317
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:214 → 271
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:1 → 23
      Requiem_N; N-terminal domain of DPF2/REQ

    3. NM_001289978.2 → NP_001276907.2  zinc finger protein neuro-d4 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (d).
      Source sequence(s)
      AC011479, GQ358728
      Consensus CDS
      CCDS92608.1
      UniProtKB/TrEMBL
      C8C3P2, Q6PJ73
      Related
      ENSP00000483226.1, ENST00000614244.4
      Conserved Domains (4) summary
      COG5189
      Location:185 → 219
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:327 → 382
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:269 → 326
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:12 → 78
      Requiem_N; N-terminal domain of DPF2/REQ

    4. NM_001363579.1 → NP_001350508.1  zinc finger protein neuro-d4 isoform e

      Status: VALIDATED

      Source sequence(s)
      AC011479, AI885717, AK094632, AL529673, AL538568, BC021191, BG702835
      Consensus CDS
      CCDS86760.1
      UniProtKB/TrEMBL
      J3KQY6, Q6PJ73
      Related
      ENSP00000411569.1, ENST00000456296.5
      Conserved Domains (4) summary
      COG5189
      Location:186 → 220
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:328 → 373
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:270 → 327
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:13 → 79
      Requiem_N; N-terminal domain of DPF2/REQ

    5. NM_004647.4 → NP_004638.3  zinc finger protein neuro-d4 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 4. The encoded protein (isoform b) is shorter, compared to isoform d.
      Source sequence(s)
      AC011479, U43843
      Consensus CDS
      CCDS33008.3
      UniProtKB/TrEMBL
      A0A804CYY4
      Related
      ENSP00000397354.3, ENST00000420980.8
      Conserved Domains (3) summary
      cd15530
      Location:283 → 338
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:225 → 282
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:12 → 78
      Requiem_N; N-terminal domain of DPF2/REQ

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      38211006..38229695 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005259292.6 → XP_005259349.1  zinc finger protein neuro-d4 isoform X11

      See identical proteins and their annotated locations for XP_005259349.1

      UniProtKB/TrEMBL
      Q6PJ73
      Conserved Domains (4) summary
      COG5189
      Location:184 → 218
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:309 → 354
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:251 → 308
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:13 → 79
      Requiem_N; N-terminal domain of DPF2/REQ

    2. XM_011527357.3 → XP_011525659.1  zinc finger protein neuro-d4 isoform X8

      See identical proteins and their annotated locations for XP_011525659.1

      UniProtKB/TrEMBL
      Q6PJ73
      Conserved Domains (4) summary
      COG5189
      Location:184 → 218
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:309 → 364
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:251 → 308
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:13 → 79
      Requiem_N; N-terminal domain of DPF2/REQ

    3. XM_024451731.2 → XP_024307499.1  zinc finger protein neuro-d4 isoform X4

      UniProtKB/TrEMBL
      Q6PJ73
      Conserved Domains (4) summary
      COG5189
      Location:184 → 218
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:326 → 371
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:268 → 325
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:13 → 79
      Requiem_N; N-terminal domain of DPF2/REQ

    4. XM_006723408.4 → XP_006723471.1  zinc finger protein neuro-d4 isoform X2

      UniProtKB/TrEMBL
      Q6PJ73
      Conserved Domains (4) summary
      COG5189
      Location:184 → 218
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:326 → 381
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:268 → 325
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:13 → 79
      Requiem_N; N-terminal domain of DPF2/REQ

    5. XM_047439493.1 → XP_047295449.1  zinc finger protein neuro-d4 isoform X9

    6. XM_047439492.1 → XP_047295448.1  zinc finger protein neuro-d4 isoform X6

    7. XM_006723407.3 → XP_006723470.1  zinc finger protein neuro-d4 isoform X1

      See identical proteins and their annotated locations for XP_006723470.1

      UniProtKB/TrEMBL
      E9PDV3, Q6PJ73
      Related
      ENSP00000390223.1, ENST00000416611.5
      Conserved Domains (4) summary
      COG5189
      Location:186 → 220
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:328 → 383
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:270 → 327
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:13 → 79
      Requiem_N; N-terminal domain of DPF2/REQ

    8. XM_047439491.1 → XP_047295447.1  zinc finger protein neuro-d4 isoform X5

    9. XM_047439490.1 → XP_047295446.1  zinc finger protein neuro-d4 isoform X3

    10. XM_005259289.3 → XP_005259346.2  zinc finger protein neuro-d4 isoform X10

    11. XM_011527356.2 → XP_011525658.2  zinc finger protein neuro-d4 isoform X7

    12. XM_011527358.3 → XP_011525660.1  zinc finger protein neuro-d4 isoform X12

      See identical proteins and their annotated locations for XP_011525660.1

      UniProtKB/TrEMBL
      Q6PJ73
      Conserved Domains (4) summary
      COG5189
      Location:130 → 164
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:272 → 327
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:214 → 271
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:1 → 23
      Requiem_N; N-terminal domain of DPF2/REQ

    13. XM_006723409.3 → XP_006723472.1  zinc finger protein neuro-d4 isoform X13

      See identical proteins and their annotated locations for XP_006723472.1

      Conserved Domains (2) summary
      cd15530
      Location:172 → 227
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cl22851
      Location:114 → 171
      PHD_SF; PHD finger superfamily

    14. XM_006723410.2 → XP_006723473.1  zinc finger protein neuro-d4 isoform X13

      See identical proteins and their annotated locations for XP_006723473.1

      Conserved Domains (2) summary
      cd15530
      Location:172 → 227
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cl22851
      Location:114 → 171
      PHD_SF; PHD finger superfamily

    15. XM_047439494.1 → XP_047295450.1  zinc finger protein neuro-d4 isoform X14

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      41013164..41031861 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322283.1 → XP_054178258.1  zinc finger protein neuro-d4 isoform X11

    2. XM_054322280.1 → XP_054178255.1  zinc finger protein neuro-d4 isoform X8

    3. XM_054322276.1 → XP_054178251.1  zinc finger protein neuro-d4 isoform X4

    4. XM_054322274.1 → XP_054178249.1  zinc finger protein neuro-d4 isoform X2

    5. XM_054322281.1 → XP_054178256.1  zinc finger protein neuro-d4 isoform X9

    6. XM_054322278.1 → XP_054178253.1  zinc finger protein neuro-d4 isoform X6

    7. XM_054322273.1 → XP_054178248.1  zinc finger protein neuro-d4 isoform X1

      UniProtKB/TrEMBL
      E9PDV3

    8. XM_054322277.1 → XP_054178252.1  zinc finger protein neuro-d4 isoform X5

    9. XM_054322275.1 → XP_054178250.1  zinc finger protein neuro-d4 isoform X3

    10. XM_054322282.1 → XP_054178257.1  zinc finger protein neuro-d4 isoform X10

    11. XM_054322279.1 → XP_054178254.1  zinc finger protein neuro-d4 isoform X7

    12. XM_054322284.1 → XP_054178259.1  zinc finger protein neuro-d4 isoform X12

    13. XM_054322285.1 → XP_054178260.1  zinc finger protein neuro-d4 isoform X13

    14. XM_054322286.1 → XP_054178261.1  zinc finger protein neuro-d4 isoform X13

    15. XM_054322287.1 → XP_054178262.1  zinc finger protein neuro-d4 isoform X14

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92782.3 GenPept UniProtKB/Swiss-Prot:Q92782

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