U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

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

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
Preferred Names
zinc finger protein 559
Names
putative protein product of Nbla00121

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous