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

Gene ID: 56242, updated on 2-Nov-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, Nov 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: 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. 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)

Genotypes

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

Gene LinkOut

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