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    ZFP64 ZFP64 zinc finger protein [ Homo sapiens (human) ]

    Gene ID: 55734, updated on 3-Nov-2024

    Summary

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    Official Symbol
    ZFP64provided by HGNC
    Official Full Name
    ZFP64 zinc finger proteinprovided by HGNC
    Primary source
    HGNC:HGNC:15940
    See related
    Ensembl:ENSG00000020256 MIM:618111; AllianceGenome:HGNC:15940
    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
    ZNF338
    Summary
    Predicted to enable DNA binding activity and metal ion binding activity. Involved in mesenchymal cell differentiation. Located in cytoplasm and megasporocyte nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 2.7), ovary (RPKM 2.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZFP64 in Genome Data Viewer
    Location:
    20q13.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (52084011..52191779, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (53855448..53963220, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (50700550..50808318, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr20:50523831-50524007 Neighboring gene RNA, U6 small nuclear 347, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50573503-50574010 Neighboring gene RNA, U7 small nuclear 6 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50576428-50577262 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50577263-50578095 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50585067-50585568 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50585569-50586068 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:50664393-50664912 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:50664913-50665430 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:50665431-50665949 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:50665950-50666467 Neighboring gene uncharacterized LOC105372664 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50721212-50722180 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50722181-50723147 Neighboring gene endoplasmic reticulum lumenal protein 29 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18117 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:50803075-50803576 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50807173-50808029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18118 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:50820158-50820351 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:50825698-50826328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50826513-50827047 Neighboring gene uncharacterized LOC105372666 Neighboring gene uncharacterized LOC107985427 Neighboring gene uncharacterized LOC105372667

    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. Function and mechanism exploration of zinc finger protein 64 in lung adenocarcinoma cell growth and metastasis. Jiang J, et al. J Recept Signal Transduct Res, 2021 Oct. PMID 33054540
    2. A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence. Lu B, et al. Cancer Cell, 2018 Dec 10. PMID 30503706, Free PMC Article
    3. ZFP64::NCOA3 gene fusion defines a novel subset of spindle cell rhabdomyosarcoma. Han R, et al. Genes Chromosomes Cancer, 2022 Nov. PMID 35521817, Free PMC Article
    4. ZFP64 transcriptionally activates PD-1 and CTLA-4 and plays an oncogenic role in esophageal cancer. Qiu G, et al. Biochem Biophys Res Commun, 2022 Sep 24. PMID 35843097
    5. Zfp64 participates in Notch signaling and regulates differentiation in mesenchymal cells. Sakamoto K, et al. J Cell Sci, 2008 May 15. PMID 18430783

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZFP64::NCOA3 gene fusion defines a novel subset of spindle cell rhabdomyosarcoma.
      Title: ZFP64::NCOA3 gene fusion defines a novel subset of spindle cell rhabdomyosarcoma.
    2. ZFP64 transcriptionally activates PD-1 and CTLA-4 and plays an oncogenic role in esophageal cancer.
      Title: ZFP64 transcriptionally activates PD-1 and CTLA-4 and plays an oncogenic role in esophageal cancer.
    3. Function and mechanism exploration of zinc finger protein 64 in lung adenocarcinoma cell growth and metastasis.
      Title: Function and mechanism exploration of zinc finger protein 64 in lung adenocarcinoma cell growth and metastasis.
    4. Data indicate zinc finger protein 64 (ZFP64) as an essential transcription factor in mixed-lineage leukemia protein (MLL)-rearranged leukemia.
      Title: A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence.
    5. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: A three-stage genome-wide association study of general cognitive ability: hunting the small effects.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC940

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mesenchymal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in megasporocyte nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 64
    Names
    zinc finger protein 338
    zinc finger protein 64 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_001319146.2 → NP_001306075.1  zinc finger protein 64 isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) represents the use of a downstream promoter and therefore differs in the 5' UTR and 5' coding region compared to variant 4. These differences cause translation initiation at an alternate start codon and result in an isoform (e) with a shorter and distinct N-terminus compared to isoform d.
      Source sequence(s)
      AK022690, BC021087, DA731353
      Consensus CDS
      CCDS82630.1
      UniProtKB/Swiss-Prot
      Q9NTW7
      Related
      ENSP00000360578.4, ENST00000371523.8
      Conserved Domains (3) summary
      COG5048
      Location:95 → 226
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:113 → 133
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:278 → 298
      ZF_C2H2; C2H2 Zn finger [structural motif]

    2. NM_018197.3 → NP_060667.2  zinc finger protein 64 isoform a

      See identical proteins and their annotated locations for NP_060667.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks several exons and includes an alternate 3' terminal exon resulting in a novel 3' coding region and 3' UTR compared to variant 4. The encoded isoform (a) has a longer and distinct C-terminus compared to isoform d.
      Source sequence(s)
      AK001744, BC041622
      Consensus CDS
      CCDS13440.1
      UniProtKB/Swiss-Prot
      Q9NPA5
      Related
      ENSP00000216923.4, ENST00000216923.5
      Conserved Domains (4) summary
      COG5048
      Location:151 → 450
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:177 → 197
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:161 → 186
      zf-H2C2_2; Zinc-finger double domain
      pfam13912
      Location:425 → 450
      zf-C2H2_6; C2H2-type zinc finger

    3. NM_022088.5 → NP_071371.3  zinc finger protein 64 isoform b

      See identical proteins and their annotated locations for NP_071371.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, lacks several exons and includes an alternate 3' terminal exon resulting in a novel 3' coding region and 3' UTR compared to variant 4. The encoded isoform (b) is shorter and has a distinct C-terminus compared to isoform d.
      Source sequence(s)
      AK001744, BC012759
      Consensus CDS
      CCDS13441.1
      UniProtKB/Swiss-Prot
      Q9NPA5
      Related
      ENSP00000344615.4, ENST00000346617.8
      Conserved Domains (4) summary
      COG5048
      Location:97 → 396
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:123 → 143
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:107 → 132
      zf-H2C2_2; Zinc-finger double domain
      pfam13912
      Location:371 → 396
      zf-C2H2_6; C2H2-type zinc finger

    4. NM_199426.2 → NP_955458.1  zinc finger protein 64 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, lacks several exons, and includes an alternate 3' terminal exon resulting in a novel 3' coding region and 3' UTR compared to variant 4. The encoded isoform (c) is longer and has a distinct C-terminus compared to isoform d.
      Source sequence(s)
      AK001744, BC012759, BC031524, BC041622
      Consensus CDS
      CCDS13442.1
      UniProtKB/Swiss-Prot
      Q9NPA5
      Related
      ENSP00000360570.4, ENST00000371515.8
      Conserved Domains (4) summary
      COG5048
      Location:149 → 448
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:175 → 195
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:159 → 184
      zf-H2C2_2; Zinc-finger double domain
      pfam13912
      Location:423 → 448
      zf-C2H2_6; C2H2-type zinc finger

    5. NM_199427.3 → NP_955459.2  zinc finger protein 64 isoform d

      See identical proteins and their annotated locations for NP_955459.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) encodes isoform d.
      Source sequence(s)
      AL109984, BC012759, BC021087
      Consensus CDS
      CCDS13439.1
      UniProtKB/Swiss-Prot
      A2A2N4, Q53H69, Q53XQ1, Q5JWM0, Q5JWM1, Q8WU98, Q9H9P1, Q9NPA5, Q9NTS7, Q9NTW7, Q9NVH4
      Related
      ENSP00000355179.2, ENST00000361387.6
      Conserved Domains (3) summary
      COG5048
      Location:172 → 603
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:177 → 197
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:497 → 517
      ZF_C2H2; C2H2 Zn finger [structural motif]

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      52084011..52191779 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440285.1 → XP_047296241.1  zinc finger protein 64 isoform X4

    2. XM_017027945.3 → XP_016883434.1  zinc finger protein 64 isoform X1

    3. XM_017027947.3 → XP_016883436.1  zinc finger protein 64 isoform X3

      Conserved Domains (3) summary
      COG5048
      Location:118 → 549
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:123 → 143
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:262 → 287
      zf-H2C2_2; Zinc-finger double domain

    4. XM_006723822.3 → XP_006723885.1  zinc finger protein 64 isoform X6

      Conserved Domains (3) summary
      COG5048
      Location:117 → 248
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:135 → 155
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:119 → 144
      zf-H2C2_2; Zinc-finger double domain

    5. XM_017027946.3 → XP_016883435.1  zinc finger protein 64 isoform X2

    6. XM_047440286.1 → XP_047296242.1  zinc finger protein 64 isoform X5

      UniProtKB/TrEMBL
      B3KQX0

    7. XM_005260449.2 → XP_005260506.1  zinc finger protein 64 isoform X5

      See identical proteins and their annotated locations for XP_005260506.1

      UniProtKB/TrEMBL
      B3KQX0
      Conserved Domains (4) summary
      COG5048
      Location:26 → 292
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:19 → 39
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:3 → 28
      zf-H2C2_2; Zinc-finger double domain
      pfam13912
      Location:267 → 292
      zf-C2H2_6; C2H2-type zinc finger

    8. XM_017027948.3 → XP_016883437.1  zinc finger protein 64 isoform X5

      UniProtKB/TrEMBL
      B3KQX0
      Conserved Domains (4) summary
      COG5048
      Location:26 → 292
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:19 → 39
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:3 → 28
      zf-H2C2_2; Zinc-finger double domain
      pfam13912
      Location:267 → 292
      zf-C2H2_6; C2H2-type zinc finger

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      53855448..53963220 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323673.1 → XP_054179648.1  zinc finger protein 64 isoform X4

    2. XM_054323670.1 → XP_054179645.1  zinc finger protein 64 isoform X1

    3. XM_054323672.1 → XP_054179647.1  zinc finger protein 64 isoform X3

    4. XM_054323677.1 → XP_054179652.1  zinc finger protein 64 isoform X6

    5. XM_054323671.1 → XP_054179646.1  zinc finger protein 64 isoform X2

    6. XM_054323676.1 → XP_054179651.1  zinc finger protein 64 isoform X5

      UniProtKB/TrEMBL
      B3KQX0

    7. XM_054323675.1 → XP_054179650.1  zinc finger protein 64 isoform X5

      UniProtKB/TrEMBL
      B3KQX0

    8. XM_054323674.1 → XP_054179649.1  zinc finger protein 64 isoform X5

      UniProtKB/TrEMBL
      B3KQX0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NTW7.3 GenPept UniProtKB/Swiss-Prot:Q9NTW7

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