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    ZNF559 zinc finger protein 559 [ Homo sapiens (human) ]

    Gene ID: 84527, updated on 11-Apr-2024

    Summary

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    Official Symbol
    ZNF559provided by HGNC
    Official Full Name
    zinc finger protein 559provided by HGNC
    Primary source
    HGNC:HGNC:28197
    See related
    Ensembl:ENSG00000188321 AllianceGenome:HGNC:28197
    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
    NBLA00121
    Summary
    Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in ovary (RPKM 6.6), endometrium (RPKM 6.0) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ZNF559 in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (9323772..9345871)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (9449983..9472081)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (9434448..9456547)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 7 subfamily H member 1 pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr19:9406829-9407424 Neighboring gene zinc finger protein 699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13927 Neighboring gene Sharpr-MPRA regulatory region 15409 Neighboring gene ZNF559-ZNF177 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10038 Neighboring gene UBXN2A pseudogene 1 Neighboring gene zinc finger protein 177

    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. AMPK Interactome Reveals New Function in Non-homologous End Joining DNA Repair. Chen Z, et al. Mol Cell Proteomics, 2020 Mar. PMID 31900314, Free PMC Article
    2. Cytoplasmic Metadherin (MTDH) provides survival advantage under conditions of stress by acting as RNA-binding protein. Meng X, et al. J Biol Chem, 2012 Feb 10. PMID 22199357, Free PMC Article
    3. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Chen S, et al. Nat Genet, 2018 Jul. PMID 29892012, Free PMC Article
    4. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073
    5. Next-generation sequencing to generate interactome datasets. Yu H, et al. Nat Methods, 2011 Jun. PMID 21516116, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough ZNF559-ZNF177

    Readthrough gene: ZNF559-ZNF177, Included gene: ZNF177

    Homology

    Clone Names

    • MGC13105

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    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 regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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 559
    Names
    putative protein product of Nbla00121

    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_001202406.1 → NP_001189335.1  zinc finger protein 559 isoform a precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AK056489, AK298169, BU608632, DA457855, DA731101
      Consensus CDS
      CCDS62531.1
      UniProtKB/TrEMBL
      A0A0A0MTT2
      Related
      ENSP00000468153.2, ENST00000587557.5
      Conserved Domains (6) summary
      smart00349
      Location:78 → 118
      KRAB; krueppel associated box
      COG5048
      Location:212 → 601
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:391 → 411
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:445 → 467
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:78 → 117
      KRAB; KRAB box
      pfam13465
      Location:431 → 454
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001202407.3 → NP_001189336.1  zinc finger protein 559 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) includes an additional exon in its 5' UTR, lacks a portion of the 5' coding region, and uses a downstream start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AC011451
      UniProtKB/TrEMBL
      B4DP29
      Conserved Domains (3) summary
      COG5048
      Location:106 → 495
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:285 → 305
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:325 → 348
      zf-H2C2_2; Zinc-finger double domain

    3. NM_001202408.1 → NP_001189337.1  zinc finger protein 559 isoform d precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site that causes a frameshift in the 3' coding region, and differs in the 3' UTR, compared to variant 1. The encoded isoform (d) has a distinct and shorter C-terminus, compared to isoform a.
      Source sequence(s)
      AK298169, AK308517, BU608632, DA457855, DA731101
      UniProtKB/TrEMBL
      B4DP29
      Conserved Domains (2) summary
      smart00349
      Location:78 → 118
      KRAB; krueppel associated box
      pfam01352
      Location:78 → 117
      KRAB; KRAB box

    4. NM_001202409.2 → NP_001189338.1  zinc finger protein 559 isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) includes an additional segment in its 5' UTR, uses a distinct start codon, uses an alternate splice site that causes a frameshift in the 3' coding region, and differs in the 3' UTR, compared to variant 1. The encoded isoform (e) has distinct N- and C-termini and is shorter than isoform a.
      Source sequence(s)
      AK298169, AK310020, BU608632, DA731101
      Consensus CDS
      CCDS62532.1
      UniProtKB/TrEMBL
      A0A0A0MTS4
      Related
      ENSP00000466496.2, ENST00000592896.5
      Conserved Domains (2) summary
      smart00349
      Location:42 → 82
      KRAB; krueppel associated box
      pfam01352
      Location:42 → 81
      KRAB; KRAB box

    5. NM_001202410.2 → NP_001189339.1  zinc finger protein 559 isoform f

      See identical proteins and their annotated locations for NP_001189339.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) includes an additional exon in its 5' UTR, uses a downstream start codon, uses an alternate splice site that causes a frameshift in the 3' coding region, and differs in the 3' UTR, compared to variant 1. The encoded isoform (f) has a shorter N-terminus, a distinct C-terminus, and is overall shorter than isoform a. Variants 6, 7 and 8 all encode isoform f.
      Source sequence(s)
      AK027700, BU608632
      Consensus CDS
      CCDS59349.1
      UniProtKB/TrEMBL
      S4R3A1
      Related
      ENSP00000325393.7, ENST00000317221.11
      Conserved Domains (1) summary
      pfam01352
      Location:13 → 54
      KRAB; KRAB box

    6. NM_001202411.2 → NP_001189340.1  zinc finger protein 559 isoform f

      See identical proteins and their annotated locations for NP_001189340.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) includes an additional exon in its 5' UTR, uses a downstream start codon, uses an alternate splice site that causes a frameshift in the 3' coding region, and differs in the 3' UTR, compared to variant 1. The encoded isoform (f) has a shorter N-terminus, a distinct C-terminus, and is overall shorter than isoform a. Variants 6, 7 and 8 all encode isoform f.
      Source sequence(s)
      AC011451
      Consensus CDS
      CCDS59349.1
      UniProtKB/TrEMBL
      S4R3A1
      Conserved Domains (1) summary
      pfam01352
      Location:13 → 54
      KRAB; KRAB box

    7. NM_001202412.2 → NP_001189341.1  zinc finger protein 559 isoform f

      See identical proteins and their annotated locations for NP_001189341.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) includes two alternate exons in its 5' UTR, uses a downstream start codon, uses an alternate splice site that causes a frameshift in the 3' coding region, and differs in the 3' UTR, compared to variant 1. The encoded isoform (f) has a shorter N-terminus, a distinct C-terminus, and is overall shorter than isoform a. Variants 6, 7 and 8 all encode isoform f.
      Source sequence(s)
      AC011451, AK027700, BP337457, BU608632, DA509657, DB158737
      Consensus CDS
      CCDS59349.1
      UniProtKB/TrEMBL
      S4R3A1
      Related
      ENSP00000468299.1, ENST00000592298.5
      Conserved Domains (1) summary
      pfam01352
      Location:13 → 54
      KRAB; KRAB box

    8. NM_032497.3 → NP_115886.1  zinc finger protein 559 isoform b

      See identical proteins and their annotated locations for NP_115886.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) includes an additional exon in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AC011451, AK298169, BU608632, CF597362
      Consensus CDS
      CCDS12211.1
      UniProtKB/Swiss-Prot
      K7EMG6, Q9BR84
      Related
      ENSP00000474760.1, ENST00000603380.6
      Conserved Domains (3) summary
      COG5048
      Location:148 → 537
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:327 → 347
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:13 → 54
      KRAB; KRAB box

    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
      9323772..9345871
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      9449983..9472081
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BR84.1 GenPept UniProtKB/Swiss-Prot:Q9BR84

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