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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

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