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    ZNF253 zinc finger protein 253 [ Homo sapiens (human) ]

    Gene ID: 56242, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ZNF253provided by HGNC
    Official Full Name
    zinc finger protein 253provided by HGNC
    Primary source
    HGNC:HGNC:13497
    See related
    Ensembl:ENSG00000256771 MIM:606954; AllianceGenome:HGNC:13497
    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
    BMZF1; BMZF-1; ZNF411
    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, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 6.0), ovary (RPKM 4.3) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ZNF253 in Genome Data Viewer
    Location:
    19p13.11
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19865830..19894674)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (20003565..20032408)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19976639..20005483)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 56, pseudogene Neighboring gene iron-sulfur cluster assembly 1 pseudogene 5 Neighboring gene uncharacterized LOC124904664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19971698-19972248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14375 Neighboring gene BCL2 interacting protein 3 pseudogene 9 Neighboring gene BCL2 interacting protein 3 pseudogene 10 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:20011859-20012408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:20012957-20013506 Neighboring gene BNIP3 pseudogene 47 Neighboring gene zinc finger protein 93 Neighboring gene uncharacterized LOC124904665 Neighboring gene BCL2 interacting protein 3 pseudogene 12

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. LDOC1, a novel MZF-1-interacting protein, induces apoptosis. Inoue M, et al. FEBS Lett, 2005 Jan 31. PMID 15670815
    2. Molecular cloning of six novel Krüppel-like zinc finger genes from hematopoietic cells and identification of a novel transregulatory domain KRNB. Han ZG, et al. J Biol Chem, 1999 Dec 10. PMID 10585455
    3. 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
    4. 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
    5. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Huttlin EL, et al. Cell, 2021 May 27. PMID 33961781, Free PMC Article

    See all (7) 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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: ZNF56P

    Homology

    Clone Names

    • FLJ90391

    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 negative regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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 253
    Names
    DNA-binding protein
    bone marrow zinc finger 1
    zinc finger protein 411

    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_001331133.1 → NP_001318062.1  zinc finger protein 253 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      BC014148, BU567590, DA167341
      UniProtKB/Swiss-Prot
      O75346

    2. NM_001331134.1 → NP_001318063.1  zinc finger protein 253 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate exons compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      BC014148, DA167341
      Consensus CDS
      CCDS86729.1
      UniProtKB/Swiss-Prot
      O75346
      Related
      ENSP00000347868.4, ENST00000355650.4
      Conserved Domains (2) summary
      COG5048
      Location:94 → 421
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:98 → 118
      ZF_C2H2; C2H2 Zn finger [structural motif]

    3. NM_021047.3 → NP_066385.2  zinc finger protein 253 isoform 1

      See identical proteins and their annotated locations for NP_066385.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC011477, BC014148
      Consensus CDS
      CCDS42532.1
      UniProtKB/Swiss-Prot
      A4FVA7, O75346, Q0P6G3, Q6P0L2, Q8NCA3, Q8NCF9
      Related
      ENSP00000468720.1, ENST00000589717.2
      Conserved Domains (5) summary
      smart00349
      Location:4 → 62
      KRAB; krueppel associated box
      COG5048
      Location:170 → 497
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:174 → 194
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:6 → 43
      KRAB; KRAB box
      pfam13465
      Location:214 → 239
      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
      19865830..19894674
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      20003565..20032408
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75346.2 GenPept UniProtKB/Swiss-Prot:O75346

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