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

Gene ID: 8193, updated on 3-Apr-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 negative regulation of transcription, DNA-templated; nervous system development; and positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be part of nBAF complex. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
19q13.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (38211006..38229695, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (41013164..41031861, complement)
105.20220307 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
  • 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 (33) 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)

Genotypes

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 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 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
part_of chromatin NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
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 

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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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_2023_10

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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