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    ZNF562 zinc finger protein 562 [ Homo sapiens (human) ]

    Gene ID: 54811, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ZNF562provided by HGNC
    Official Full Name
    zinc finger protein 562provided by HGNC
    Primary source
    HGNC:HGNC:25950
    See related
    Ensembl:ENSG00000171466 AllianceGenome:HGNC:25950
    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 factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in esophagus (RPKM 4.1), urinary bladder (RPKM 3.4) and 25 other tissues See more
    Orthologs
    all
    NEW
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    Genomic context

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    See ZNF562 in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (9641807..9675100, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (9768019..9801288, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (9752483..9785776, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 561 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:9731087-9731669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13932 Neighboring gene ZNF561 antisense RNA 1 (head to head) Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:9784745-9785944 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:9785983-9786982 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:9791103-9791685 Neighboring gene ribosomal protein S4X pseudogene 22 Neighboring gene zinc finger protein 812, pseudogene

    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 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. Gene expression profile of human bone marrow stromal cells: high-throughput expressed sequence tag sequencing analysis. Jia L, et al. Genomics, 2002 Jan. PMID 11827452
    2. Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells. Chang YJ, et al. Int J Mol Sci, 2023 Jun 6. PMID 37372979, Free PMC Article
    3. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Suzuki Y, et al. Genome Res, 2004 Sep. PMID 15342556, Free PMC Article
    4. Ubiquitin-mediated proteolysis of HuR by heat shock. Abdelmohsen K, et al. EMBO J, 2009 May 6. PMID 19322201, Free PMC Article
    5. Cullin 3 Exon 9 Deletion in Familial Hyperkalemic Hypertension Impairs Cullin3-Ring-E3 Ligase (CRL3) Dynamic Regulation and Cycling. Kouranti I, et al. Int J Mol Sci, 2022 May 5. PMID 35563538, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20079, MGC126160

    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 cis-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 DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 562

    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_001130031.2 → NP_001123503.1  zinc finger protein 562 isoform a

      See identical proteins and their annotated locations for NP_001123503.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer protein (isoform a). Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC008759, AI753280, BP221824, DC405554
      Consensus CDS
      CCDS45956.1
      UniProtKB/Swiss-Prot
      Q32MN2, Q6V9R5, Q9NXS5
      Related
      ENSP00000410734.1, ENST00000453372.7
      Conserved Domains (4) summary
      COG5048
      Location:258 → 420
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:318 → 338
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:181 → 198
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:40 → 81
      KRAB; KRAB box

    2. NM_001130032.2 → NP_001123504.1  zinc finger protein 562 isoform a

      See identical proteins and their annotated locations for NP_001123504.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses a different splice site in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC008759, AI753280, BP221824, DC403290
      Consensus CDS
      CCDS45956.1
      UniProtKB/Swiss-Prot
      Q32MN2, Q6V9R5, Q9NXS5
      Conserved Domains (4) summary
      COG5048
      Location:258 → 420
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:318 → 338
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:181 → 198
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:40 → 81
      KRAB; KRAB box

    3. NM_001300885.2 → NP_001287814.1  zinc finger protein 562 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform c, which is shorter by an amino acid, compared to isoform a.
      Source sequence(s)
      AC008759, AI753280, AK297446, AK304370, BC109062
      Consensus CDS
      CCDS74280.1
      UniProtKB/TrEMBL
      K7EIE6
      Related
      ENSP00000464716.1, ENST00000590155.5
      Conserved Domains (7) summary
      smart00349
      Location:41 → 85
      KRAB; krueppel associated box
      COG5048
      Location:257 → 419
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:317 → 337
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:180 → 197
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:287 → 309
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:41 → 80
      KRAB; KRAB box
      pfam13465
      Location:358 → 382
      zf-H2C2_2; Zinc-finger double domain

    4. NM_017656.4 → NP_060126.2  zinc finger protein 562 isoform b

      See identical proteins and their annotated locations for NP_060126.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks alternate segments in the 5' coding region, compared to variant 1. The resulting protein (isoform b) has a shorter N-terminus when it is compared to isoform a.
      Source sequence(s)
      AC008759, AI753280, AK000086, BP221824
      Consensus CDS
      CCDS12217.1
      UniProtKB/Swiss-Prot
      Q6V9R5
      Related
      ENSP00000293648.3, ENST00000293648.8
      Conserved Domains (3) summary
      COG5048
      Location:186 → 348
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:246 → 266
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:287 → 311
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      9641807..9675100 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438996.1 → XP_047294952.1  zinc finger protein 562 isoform X3

    2. XM_047438995.1 → XP_047294951.1  zinc finger protein 562 isoform X2

    3. XM_017026898.3 → XP_016882387.1  zinc finger protein 562 isoform X1

      UniProtKB/TrEMBL
      K7EIE6
      Conserved Domains (7) summary
      smart00349
      Location:41 → 85
      KRAB; krueppel associated box
      COG5048
      Location:257 → 419
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:317 → 337
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:180 → 197
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:287 → 309
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:41 → 80
      KRAB; KRAB box
      pfam13465
      Location:358 → 382
      zf-H2C2_2; Zinc-finger double domain

    4. XM_047438994.1 → XP_047294950.1  zinc finger protein 562 isoform X1

      UniProtKB/TrEMBL
      K7EIE6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      9768019..9801288 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321307.1 → XP_054177282.1  zinc finger protein 562 isoform X3

    2. XM_054321306.1 → XP_054177281.1  zinc finger protein 562 isoform X2

    3. XM_054321304.1 → XP_054177279.1  zinc finger protein 562 isoform X1

      UniProtKB/TrEMBL
      K7EIE6

    4. XM_054321305.1 → XP_054177280.1  zinc finger protein 562 isoform X1

      UniProtKB/TrEMBL
      K7EIE6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6V9R5.2 GenPept UniProtKB/Swiss-Prot:Q6V9R5

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