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    ZNF487 zinc finger protein 487 [ Homo sapiens (human) ]

    Gene ID: 642819, updated on 11-Apr-2024

    Summary

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    Official Symbol
    ZNF487provided by HGNC
    Official Full Name
    zinc finger protein 487provided by HGNC
    Primary source
    HGNC:HGNC:23488
    See related
    Ensembl:ENSG00000243660 AllianceGenome:HGNC:23488
    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
    KRBO1; ZNF487P
    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. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 13.6), gall bladder (RPKM 2.0) and 18 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ZNF487 in Genome Data Viewer
    Location:
    10q11.21
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (43436848..43523894)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (44317784..44405853)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (43932296..43978629)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2331 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:43916126-43916862 Neighboring gene long intergenic non-protein coding RNA 2916 Neighboring gene small nucleolar RNA, C/D box 3J Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2332 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr10:43950240-43951128 and GRCh37_chr10:43951129-43952017 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr10:43953391-43953946 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:43959685-43960348 Neighboring gene RNA, U7 small nuclear 193 pseudogene Neighboring gene zinc finger protein 12 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr10:44039642-44040155 Neighboring gene zinc finger protein 239 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3303 Neighboring gene coiled-coil-helix-coiled-coil-helix domain-containing protein 2-like

    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. New interaction partners for Nek4.1 and Nek4.2 isoforms: from the DNA damage response to RNA splicing. Basei FL, et al. Proteome Sci, 2015. PMID 25798074, Free PMC Article
    2. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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

    Homology

    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 DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    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
    		  
    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
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    putative zinc finger protein 487
    Names
    KRAB domain only 1
    KRAB domain only protein 1
    zinc finger protein 487, pseudogene

    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_001355444.3 → NP_001342373.2  putative zinc finger protein 487 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL450326
      Consensus CDS
      CCDS86084.2
      UniProtKB/TrEMBL
      A0A494C0H0
      Related
      ENSP00000392335.2, ENST00000437590.4
      Conserved Domains (2) summary
      sd00019
      Location:158 → 174
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl02581
      Location:1 → 32
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    2. NM_001355445.3 → NP_001342374.2  putative zinc finger protein 487 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL450326
      Consensus CDS
      CCDS86084.2
      UniProtKB/TrEMBL
      A0A494C0H0
      Related
      ENSP00000314093.8, ENST00000315429.12
      Conserved Domains (2) summary
      sd00019
      Location:158 → 174
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl02581
      Location:1 → 32
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    3. NM_001355446.3 → NP_001342375.2  putative zinc finger protein 487 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL450326
      Consensus CDS
      CCDS86084.2
      UniProtKB/TrEMBL
      A0A494C0H0
      Conserved Domains (2) summary
      sd00019
      Location:158 → 174
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl02581
      Location:1 → 32
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    4. NM_001355447.2 → NP_001342376.1  putative zinc finger protein 487 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL450326
      Conserved Domains (2) summary
      sd00019
      Location:162 → 178
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:7 → 48
      KRAB; KRAB box

    5. NM_001355448.2 → NP_001342377.1  putative zinc finger protein 487 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL450326
      Conserved Domains (2) summary
      smart00349
      Location:8 → 68
      KRAB; krueppel associated box
      sd00019
      Location:194 → 210
      ZF_C2H2; C2H2 Zn finger [structural motif]

    6. NM_001355449.2 → NP_001342378.1  putative zinc finger protein 487 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL450326
      Conserved Domains (1) summary
      sd00019
      Location:127 → 143
      ZF_C2H2; C2H2 Zn finger [structural motif]

    7. NM_001355450.1 → NP_001342379.1  putative zinc finger protein 487 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL450326
      Conserved Domains (1) summary
      sd00019
      Location:127 → 143
      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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      43436848..43523894
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425633.1 → XP_047281589.1  putative zinc finger protein 487 isoform X3

    2. XM_047425631.1 → XP_047281587.1  putative zinc finger protein 487 isoform X3

    3. XM_047425632.1 → XP_047281588.1  putative zinc finger protein 487 isoform X3

      Related
      ENSP00000510544.1, ENST00000689627.1

    4. XM_047425630.1 → XP_047281586.1  putative zinc finger protein 487 isoform X3

    5. XM_047425629.1 → XP_047281585.1  putative zinc finger protein 487 isoform X3

    6. XM_024448132.2 → XP_024303900.1  putative zinc finger protein 487 isoform X3

      Conserved Domains (2) summary
      sd00019
      Location:159 → 175
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl02581
      Location:2 → 33
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    7. XM_024448131.2 → XP_024303899.1  putative zinc finger protein 487 isoform X2

      Conserved Domains (2) summary
      sd00019
      Location:163 → 179
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:8 → 49
      KRAB; KRAB box

    8. XM_024448129.2 → XP_024303897.1  putative zinc finger protein 487 isoform X1

      Conserved Domains (2) summary
      smart00349
      Location:9 → 69
      KRAB; krueppel associated box
      sd00019
      Location:195 → 211
      ZF_C2H2; C2H2 Zn finger [structural motif]

    RNA

    1. XR_007061981.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      44317784..44405853
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366553.1 → XP_054222528.1  putative zinc finger protein 487 isoform X3

    2. XM_054366561.1 → XP_054222536.1  putative zinc finger protein 487 isoform X3

    3. XM_054366551.1 → XP_054222526.1  putative zinc finger protein 487 isoform X3

    4. XM_054366552.1 → XP_054222527.1  putative zinc finger protein 487 isoform X3

    5. XM_054366556.1 → XP_054222531.1  putative zinc finger protein 487 isoform X5

    6. XM_054366560.1 → XP_054222535.1  putative zinc finger protein 487 isoform X3

    7. XM_054366555.1 → XP_054222530.1  putative zinc finger protein 487 isoform X4

    8. XM_054366558.1 → XP_054222533.1  putative zinc finger protein 487 isoform X6

    9. XM_054366559.1 → XP_054222534.1  putative zinc finger protein 487 isoform X3

    10. XM_054366557.1 → XP_054222532.1  putative zinc finger protein 487 isoform X2

    11. XM_054366554.1 → XP_054222529.1  putative zinc finger protein 487 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B1APH4.3 GenPept UniProtKB/Swiss-Prot:B1APH4

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    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials