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    DPF2 double PHD fingers 2 [ Homo sapiens (human) ]

    Gene ID: 5977, updated on 5-May-2024

    Summary

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    Official Symbol
    DPF2provided by HGNC
    Official Full Name
    double PHD fingers 2provided by HGNC
    Primary source
    HGNC:HGNC:9964
    See related
    Ensembl:ENSG00000133884 MIM:601671; AllianceGenome:HGNC:9964
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    REQ; CSS7; UBID4; ubi-d4; SMARCG2
    Summary
    The protein encoded by this gene is a member of the d4 domain family, characterized by a zinc finger-like structural motif. This protein functions as a transcription factor which is necessary for the apoptotic response following deprivation of survival factors. It likely serves a regulatory role in rapid hematopoietic cell growth and turnover. This gene is considered a candidate gene for multiple endocrine neoplasia type I, an inherited cancer syndrome involving multiple parathyroid, enteropancreatic, and pituitary tumors. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 23.7), ovary (RPKM 23.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    11q13.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65333852..65354262)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65327170..65347565)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (65101323..65121733)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3513 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3514 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3515 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:65086579-65086802 Neighboring gene CDC42 effector protein 2 Neighboring gene uncharacterized LOC124902691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4953 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65104413-65104913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3518 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3519 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3521 Neighboring gene Sharpr-MPRA regulatory region 3865 Neighboring gene tigger transposable element derived 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65144096-65144596 Neighboring gene FERM domain containing 8 Neighboring gene solute carrier family 25 member 45 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:65149420-65150619 Neighboring gene Sharpr-MPRA regulatory region 10780

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. BAF45D knockdown decreases cell viability, inhibits colony formation, induces cell apoptosis and S-phase arrest in human pancreatic cancer cells.
      Title: BAF45D knockdown decreases cell viability, inhibits colony formation, induces cell apoptosis and S-phase arrest in human pancreatic cancer cells.
    2. de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant-negative mechanism of pathogenicity.
      Title: Mutations in the BAF-Complex Subunit DPF2 Are Associated with Coffin-Siris Syndrome.
    3. Authors show that DPF2 interacts with the acetylated tails of both histones 3 and 4 via bipartite binding pockets on the DPF2 surface. Blocking these interactions through targeted mutagenesis of DPF2 abolishes its recruitment to target chromatin regions as well as its ability to prevent myeloid differentiation in vivo.
      Title: Histone-binding of DPF2 mediates its repressive role in myeloid differentiation.
    4. Upon influenza virus infection, DPF2 dysregulated IFN-beta induction and expression of cytokines/chemokines and antiviral proteins. This study provides evidence that influenza virus utilizes DPF2 to escape host innate immunity.
      Title: Double Plant Homeodomain Fingers 2 (DPF2) Promotes the Immune Escape of Influenza Virus by Suppressing Beta Interferon Production.
    5. The demonstrate that the histone acetylation-binding double PHD finger (DPF) domains of human MOZ (also known as KAT6A) and DPF2 (also known as BAF45d) accommodate a wide range of histone lysine acylation with the strongest preference for propionylation (Kcr).
      Title: Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2.
    6. the role of SMARCA4 and the two SWI/SNF subunits SMARCD2/BAF60B and DPF2/BAF45D in leukaemia, was investigated.
      Title: SWI/SNF Subunits SMARCA4, SMARCD2 and DPF2 Collaborate in MLL-Rearranged Leukaemia Maintenance.
    7. DPF2 decreases monomeric and mono-ubiquitinated OCT4, assembles poly-ubiquitin chains on OCT4 mainly through Ub-K48 linkage
      Title: DPF2 regulates OCT4 protein level and nuclear distribution.
    8. crystal structure of the C2H2-type zinc finger domain of human DPF2 with a canonical C2H2 fold, which contains two beta strands and one alpha helix, was reported.
      Title: Crystal structure of the Cys2His2-type zinc finger domain of human DPF2.
    9. found that targeting Requiem and Alg-2 did not result in extended culture viability, but resulted in an increase in maximum viable cell numbers and cumulative IVCD under fed-batch conditions
      Title: Simultaneous targeting of Requiem & Alg-2 in Chinese hamster ovary cells for improved recombinant protein production.
    10. REQ functions as an efficient adaptor protein between the SWI/SNF complex and RelB/p52 and plays important roles in noncanonical NF-kappaB transcriptional activation and its associated oncogenic activity.
      Title: Requiem protein links RelB/p52 and the Brm-type SWI/SNF complex in a noncanonical NF-kappaB pathway.
    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

    Associated conditions

    Description Tests
    Coffin-Siris syndrome 7
    MedGen: C4747954 OMIM: 618027 GeneReviews: Coffin-Siris Syndrome
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    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)

    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

    • MGC10180

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables H3K9me3 modified histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables lysine-acetylated histone binding IDA
    Inferred from Direct Assay
    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 transcription corepressor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in apoptotic signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of myeloid progenitor cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of double-strand break repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of stem cell population maintenance 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 SWI/SNF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		  
    part_of chromatin HDA PubMed 
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of chromatin NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    part_of nBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    zinc finger protein ubi-d4
    Names
    BAF45D
    BRG1-associated factor 45D
    D4, zinc and double PHD fingers family 2
    apoptosis response zinc finger protein
    protein requiem
    requiem, apoptosis response zinc finger

    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_001330308.2 → NP_001317237.1  zinc finger protein ubi-d4 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AI381588, AL555427, AP000944, BI753338, BP201169, CB045170
      Consensus CDS
      CCDS81583.1
      UniProtKB/TrEMBL
      A0A994J426, J3KMZ8
      Related
      ENSP00000252268.4, ENST00000252268.8
      Conserved Domains (4) summary
      COG5189
      Location:201 → 247
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:343 → 388
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15691
      Location:286 → 341
      PHD1_DPF2_like; PHD finger 1 found in D4, zinc and double PHD fingers family 2 (DPF2)
      pfam14051
      Location:13 → 75
      Requiem_N; N-terminal domain of DPF2/REQ

    2. NM_006268.5 → NP_006259.1  zinc finger protein ubi-d4 isoform 1

      See identical proteins and their annotated locations for NP_006259.1

      Status: REVIEWED

      Source sequence(s)
      AK313408, AP000944, BC014889
      Consensus CDS
      CCDS8100.1
      UniProtKB/Swiss-Prot
      A8K7C9, B4DT58, Q92785
      UniProtKB/TrEMBL
      A0A994J426
      Related
      ENSP00000436901.1, ENST00000528416.6
      Conserved Domains (4) summary
      COG5189
      Location:201 → 233
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:329 → 374
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15691
      Location:272 → 327
      PHD1_DPF2_like; PHD finger 1 found in D4, zinc and double PHD fingers family 2 (DPF2)
      pfam14051
      Location:13 → 75
      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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      65333852..65354262
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017018101.3 → XP_016873590.1  zinc finger protein ubi-d4 isoform X1

      UniProtKB/TrEMBL
      A0A994J426
      Conserved Domains (4) summary
      COG5189
      Location:181 → 227
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:323 → 368
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15691
      Location:266 → 321
      PHD1_DPF2_like; PHD finger 1 found in D4, zinc and double PHD fingers family 2 (DPF2)
      pfam14051
      Location:1 → 55
      Requiem_N; N-terminal domain of DPF2/REQ

    RNA

    1. XR_007062491.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      65327170..65347565
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_008488422.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92785.2 GenPept UniProtKB/Swiss-Prot:Q92785

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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