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ZNF254 zinc finger protein 254 [ Homo sapiens (human) ]

Gene ID: 9534, updated on 5-Mar-2024

Summary

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Official Symbol
ZNF254provided by HGNC
Official Full Name
zinc finger protein 254provided by HGNC
Primary source
HGNC:HGNC:13047
See related
Ensembl:ENSG00000213096 MIM:604768; AllianceGenome:HGNC:13047
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
BMZF-5; ZNF539; ZNF91L; HD-ZNF1
Summary
Zinc finger proteins have been shown to interact with nucleic acids and to have diverse functions. The zinc finger domain is a conserved amino acid sequence motif containing 2 specifically positioned cysteines and 2 histidines that are involved in coordinating zinc. Kruppel-related proteins form 1 family of zinc finger proteins. See ZFP93 (MIM 604749) for additional information on zinc finger proteins.[supplied by OMIM, Jul 2002]
Expression
Ubiquitous expression in thyroid (RPKM 5.2), ovary (RPKM 2.6) and 24 other tissues See more
Orthologs
all
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Genomic context

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Location:
19p12
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (24033449..24129968)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (24181076..24280157)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (24216251..24312770)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene RNA, 28S ribosomal pseudogene Neighboring gene Sharpr-MPRA regulatory regions 11764 and 11751 Neighboring gene Sharpr-MPRA regulatory region 3900 Neighboring gene RNA, 5.8S ribosomal pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14400 Neighboring gene BCL2 interacting protein 3 pseudogene 40 Neighboring gene long intergenic non-protein coding RNA 3085 Neighboring gene hepatitis A virus cellular receptor 1 pseudogene 1

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. Biomarkers of human cutaneous squamous cell carcinoma from tissues and cell lines identified by DNA microarrays and qRT-PCR. Dooley TP, et al. Biochem Biophys Res Commun, 2003 Jul 11. PMID 12821146
  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. Genetic association with overall survival of taxane-treated lung cancer patients - a genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study. Niu N, et al. BMC Cancer, 2012 Sep 24. PMID 23006423, Free PMC Article
  4. Identification of genes expressed in human CD34(+) hematopoietic stem/progenitor cells by expressed sequence tags and efficient full-length cDNA cloning. Mao M, et al. Proc Natl Acad Sci U S A, 1998 Jul 7. PMID 9653160, Free PMC Article
  5. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. König R, et al. Cell, 2008 Oct 3. PMID 18854154, Free PMC Article

See all (18) 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

EBI GWAS Catalog

Description
Genetic association with overall survival of taxane-treated lung cancer patients - A genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study.
EBI GWAS Catalog

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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of zinc finger protein 254 (ZNF254) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ34761, FLJ34831, FLJ35501, FLJ58216

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 transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
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 254
Names
CTD-2017D11.1
bone marrow zinc finger 5
hematopoietic cell-derived zinc finger protein 1
zinc finger protein 539

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_001278661.2 → NP_001265590.1  zinc finger protein 254 isoform a

    See identical proteins and their annotated locations for NP_001265590.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode isoform a.
    Source sequence(s)
    AC092279, AW503073, BM876253, BM976089, BU783464, BX281205, CN267605, CN395850, DA501852, DA852860, DB539972
    Consensus CDS
    CCDS74323.1
    UniProtKB/TrEMBL
    A0A087WZJ7
    Related
    ENSP00000482703.1, ENST00000613065.4
    Conserved Domains (4) summary
    smart00349
    Location:1 → 32
    KRAB; krueppel associated box
    COG5048
    Location:138 → 553
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:367 → 387
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:436 → 460
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001278662.2 → NP_001265591.1  zinc finger protein 254 isoform a

    See identical proteins and their annotated locations for NP_001265591.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode isoform a.
    Source sequence(s)
    AW503073, BM876253, BM976089, BU783464, CN267605, CN395850, DA195951, DA501852, DA852860, DB286139, DB539972
    Consensus CDS
    CCDS74323.1
    UniProtKB/TrEMBL
    A0A087WZJ7
    Conserved Domains (4) summary
    smart00349
    Location:1 → 32
    KRAB; krueppel associated box
    COG5048
    Location:138 → 553
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:367 → 387
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:436 → 460
    zf-H2C2_2; Zinc-finger double domain

  3. NM_001278663.2 → NP_001265592.1  zinc finger protein 254 isoform c

    See identical proteins and their annotated locations for NP_001265592.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon compared to variant 1. It encodes isoform c which has a shorter N-terminus compared to isoform a. Variants 5 and 6 encode isoform c.
    Source sequence(s)
    AC092279, AK303431, BM876253, BM976089, BU783464, CN395850, DB539972
    Consensus CDS
    CCDS62623.1
    UniProtKB/TrEMBL
    F5H2M4
    Conserved Domains (4) summary
    COG5048
    Location:94 → 509
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:379 → 399
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:155 → 174
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:392 → 416
    zf-H2C2_2; Zinc-finger double domain

  4. NM_001278664.2 → NP_001265593.1  zinc finger protein 254 isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon compared to variant 1. It encodes isoform d which has a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AW503073, BM876253, BM976089, BU783464, CN267605, CN395850, DA501852, DA684942, DA852860, DB539972
    Consensus CDS
    CCDS74324.1
    UniProtKB/TrEMBL
    A0A087X0A2
    Related
    ENSP00000483222.1, ENST00000611359.3
    Conserved Domains (3) summary
    COG5048
    Location:106 → 521
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:335 → 355
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:404 → 428
    zf-H2C2_2; Zinc-finger double domain

  5. NM_001278665.2 → NP_001265594.1  zinc finger protein 254 isoform e

    See identical proteins and their annotated locations for NP_001265594.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) differs in both UTRs and has multiple coding region differences, compared to variant 1. This variant encodes isoform e, which is shorter than isoform a.
    Source sequence(s)
    BC044906, BC056243
    Consensus CDS
    CCDS62622.1
    UniProtKB/TrEMBL
    Q7Z2R1
    Related
    ENSP00000341573.6, ENST00000339642.10
    Conserved Domains (1) summary
    smart00349
    Location:13 → 73
    KRAB; krueppel associated box

  6. NM_001278677.2 → NP_001265606.1  zinc finger protein 254 isoform a

    See identical proteins and their annotated locations for NP_001265606.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a. Variants 1, 2, and 3 encode isoform a.
    Source sequence(s)
    AC092279, AW503073, BM876253, BM976089, BU783464, CN267605, CN395850, DA101675, DA195951, DA501852, DA852860, DB539972
    Consensus CDS
    CCDS74323.1
    UniProtKB/TrEMBL
    A0A087WZJ7
    Conserved Domains (4) summary
    smart00349
    Location:1 → 32
    KRAB; krueppel associated box
    COG5048
    Location:138 → 553
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:367 → 387
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:436 → 460
    zf-H2C2_2; Zinc-finger double domain

  7. NM_001278678.2 → NP_001265607.1  zinc finger protein 254 isoform c

    See identical proteins and their annotated locations for NP_001265607.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon compared to variant 1. It encodes isoform c which has a shorter N-terminus compared to isoform a. Variants 5 and 6 encode isoform c.
    Source sequence(s)
    AW503073, BM876253, BM976089, BU783464, CN267605, CN395850, DA230395, DA501852, DA852860, DB539972
    Consensus CDS
    CCDS62623.1
    UniProtKB/TrEMBL
    F5H2M4
    Related
    ENSP00000484930.1, ENST00000616028.2
    Conserved Domains (4) summary
    COG5048
    Location:94 → 509
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:379 → 399
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:155 → 174
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:392 → 416
    zf-H2C2_2; Zinc-finger double domain

  8. NM_203282.4 → NP_975011.3  zinc finger protein 254 isoform b

    See identical proteins and their annotated locations for NP_975011.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region and uses an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct and longer N-terminus compared to isoform a.
    Source sequence(s)
    AF054180, BC043147, BC139749, BM876253, BM976089, BU783464, CN395850, DB340394
    Consensus CDS
    CCDS32983.1
    UniProtKB/Swiss-Prot
    A4QPC0, O75437, Q86XL7
    Related
    ENSP00000349494.3, ENST00000357002.5
    Conserved Domains (3) summary
    smart00349
    Location:13 → 73
    KRAB; krueppel associated box
    COG5048
    Location:264 → 625
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:408 → 428
    ZF_C2H2; C2H2 Zn finger [structural motif]

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
    24033449..24129968
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439750.1 → XP_047295706.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  2. XM_047439742.1 → XP_047295698.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  3. XM_047439743.1 → XP_047295699.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  4. XM_047439746.1 → XP_047295702.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  5. XM_047439752.1 → XP_047295708.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  6. XM_047439747.1 → XP_047295703.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  7. XM_047439748.1 → XP_047295704.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  8. XM_047439738.1 → XP_047295694.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  9. XM_047439739.1 → XP_047295695.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  10. XM_047439740.1 → XP_047295696.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  11. XM_047439741.1 → XP_047295697.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  12. XM_047439749.1 → XP_047295705.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  13. XM_011528443.2 → XP_011526745.1  zinc finger protein 254 isoform X1

    See identical proteins and their annotated locations for XP_011526745.1

    UniProtKB/TrEMBL
    A0A087WZJ7
    Conserved Domains (4) summary
    smart00349
    Location:1 → 32
    KRAB; krueppel associated box
    COG5048
    Location:138 → 553
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:367 → 387
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:436 → 460
    zf-H2C2_2; Zinc-finger double domain

  14. XM_011528448.4 → XP_011526750.1  zinc finger protein 254 isoform X4

    See identical proteins and their annotated locations for XP_011526750.1

    UniProtKB/TrEMBL
    F5H2M4
    Conserved Domains (4) summary
    COG5048
    Location:94 → 509
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:379 → 399
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:155 → 174
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:392 → 416
    zf-H2C2_2; Zinc-finger double domain

  15. XM_047439744.1 → XP_047295700.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  16. XM_047439745.1 → XP_047295701.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  17. XM_047439751.1 → XP_047295707.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  18. XM_047439753.1 → XP_047295709.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  19. XM_047439755.1 → XP_047295711.1  zinc finger protein 254 isoform X2

  20. XM_017027518.2 → XP_016883007.1  zinc finger protein 254 isoform X3

    UniProtKB/TrEMBL
    A0A087X0A2
    Conserved Domains (3) summary
    COG5048
    Location:106 → 521
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:335 → 355
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:404 → 428
    zf-H2C2_2; Zinc-finger double domain

  21. XM_047439754.1 → XP_047295710.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  22. XM_047439756.1 → XP_047295712.1  zinc finger protein 254 isoform X4

    UniProtKB/TrEMBL
    F5H2M4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    24181076..24280157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322733.1 → XP_054178708.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  2. XM_054322724.1 → XP_054178699.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  3. XM_054322725.1 → XP_054178700.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  4. XM_054322729.1 → XP_054178704.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  5. XM_054322735.1 → XP_054178710.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  6. XM_054322728.1 → XP_054178703.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  7. XM_054322730.1 → XP_054178705.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  8. XM_054322718.1 → XP_054178693.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  9. XM_054322720.1 → XP_054178695.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  10. XM_054322721.1 → XP_054178696.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  11. XM_054322722.1 → XP_054178697.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  12. XM_054322723.1 → XP_054178698.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  13. XM_054322731.1 → XP_054178706.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  14. XM_054322719.1 → XP_054178694.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  15. XM_054322740.1 → XP_054178715.1  zinc finger protein 254 isoform X4

    UniProtKB/TrEMBL
    F5H2M4

  16. XM_054322726.1 → XP_054178701.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  17. XM_054322727.1 → XP_054178702.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  18. XM_054322734.1 → XP_054178709.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  19. XM_054322736.1 → XP_054178711.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  20. XM_054322738.1 → XP_054178713.1  zinc finger protein 254 isoform X2

  21. XM_054322739.1 → XP_054178714.1  zinc finger protein 254 isoform X3

    UniProtKB/TrEMBL
    A0A087X0A2

  22. XM_054322732.1 → XP_054178707.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  23. XM_054322737.1 → XP_054178712.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7

  24. XM_054322741.1 → XP_054178716.1  zinc finger protein 254 isoform X4

    UniProtKB/TrEMBL
    F5H2M4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_004876.2: Suppressed sequence

    Description
    NM_004876.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75437.3 GenPept UniProtKB/Swiss-Prot:O75437

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