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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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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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Chemical Information
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