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

Gene ID: 55734, updated on 5-Mar-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. Predicted to be involved in positive regulation of cytokine production and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of mRNA splicing, via spliceosome. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (52084011..52191779, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (53855448..53963220, complement)
105.20220307 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
  • 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. 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
  3. 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
  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 (46) 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_2023_10

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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