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    ZNF560 zinc finger protein 560 [ Homo sapiens (human) ]

    Gene ID: 147741, updated on 11-Apr-2024

    Summary

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    Official Symbol
    ZNF560provided by HGNC
    Official Full Name
    zinc finger protein 560provided by HGNC
    Primary source
    HGNC:HGNC:26484
    See related
    Ensembl:ENSG00000198028 AllianceGenome:HGNC:26484
    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
    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
    Restricted expression toward testis (RPKM 2.9) See more
    Orthologs
    all
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    Genomic context

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    See ZNF560 in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (9445876..9506692, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (9572082..9632888, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (9577031..9609292, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268250 Neighboring gene zinc finger protein 266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13929 Neighboring gene uncharacterized LOC105372269 Neighboring gene uncharacterized LOC105372268 Neighboring gene actin beta pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:9648627-9649362 Neighboring gene zinc finger protein 426

    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. Screening for differentially expressed genes between left- and right-sided colon carcinoma by microarray analysis. Zhu H, et al. Oncol Lett, 2013 Aug. PMID 24137329, Free PMC Article
    2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) 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

    General gene information

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    Homology

    Clone Names

    • FLJ31986, MGC119490, MGC119493

    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
    		  
    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 560

    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.

    Genomic

    1. NG_054924.1 RefSeqGene

      Range
      13077..45338
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001351678.2 → NP_001338607.1  zinc finger protein 560 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction in the 5' end and uses a downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC008567, AK056548, BC101039
      Conserved Domains (4) summary
      smart00349
      Location:4 → 55
      KRAB; krueppel associated box
      COG5048
      Location:238 → 648
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:608 → 628
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:651 → 673
      zf-H2C2_2; Zinc-finger double domain

    2. NM_152476.3 → NP_689689.2  zinc finger protein 560 isoform 1

      See identical proteins and their annotated locations for NP_689689.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC008567, BC101040, DA744260, T41372
      Consensus CDS
      CCDS12214.1
      UniProtKB/Swiss-Prot
      Q495S9, Q495T1, Q96MR9
      Related
      ENSP00000301480.3, ENST00000301480.5
      Conserved Domains (6) summary
      smart00349
      Location:13 → 69
      KRAB; krueppel associated box
      COG5048
      Location:344 → 754
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:714 → 734
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:600 → 622
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:13 → 50
      KRAB; KRAB box
      pfam13465
      Location:726 → 751
      zf-H2C2_2; Zinc-finger double domain

    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
      9445876..9506692 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011527697.3 → XP_011525999.1  zinc finger protein 560 isoform X1

      See identical proteins and their annotated locations for XP_011525999.1

      UniProtKB/Swiss-Prot
      Q495S9, Q495T1, Q96MR9
      Conserved Domains (6) summary
      smart00349
      Location:13 → 69
      KRAB; krueppel associated box
      COG5048
      Location:344 → 754
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:714 → 734
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:600 → 622
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:13 → 50
      KRAB; KRAB box
      pfam13465
      Location:726 → 751
      zf-H2C2_2; Zinc-finger double domain

    2. XM_011527696.3 → XP_011525998.1  zinc finger protein 560 isoform X1

      See identical proteins and their annotated locations for XP_011525998.1

      UniProtKB/Swiss-Prot
      Q495S9, Q495T1, Q96MR9
      Conserved Domains (6) summary
      smart00349
      Location:13 → 69
      KRAB; krueppel associated box
      COG5048
      Location:344 → 754
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:714 → 734
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:600 → 622
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:13 → 50
      KRAB; KRAB box
      pfam13465
      Location:726 → 751
      zf-H2C2_2; Zinc-finger double domain

    RNA

    1. XR_007066601.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      9572082..9632888 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319876.1 → XP_054175851.1  zinc finger protein 560 isoform X1

      UniProtKB/Swiss-Prot
      Q495S9, Q495T1, Q96MR9

    2. XM_054319877.1 → XP_054175852.1  zinc finger protein 560 isoform X1

      UniProtKB/Swiss-Prot
      Q495S9, Q495T1, Q96MR9

    RNA

    1. XR_008485086.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96MR9.2 GenPept UniProtKB/Swiss-Prot:Q96MR9

    Gene LinkOut

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

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