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

    Gene ID: 9534, updated on 2-Nov-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
    NEW
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    Genomic context

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    See ZNF254 in Genome Data Viewer
    Location:
    19p12
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (24033449..24129968)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (24181076..24280157)
    RS_2024_09 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 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 KrĂĽppel-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)

    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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    NEW Try the new Transcript table

    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_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
      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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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