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

Gene ID: 9534, updated on 17-Jun-2019

Summary

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
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

Genomic context

See ZNF254 in Genome Data Viewer
Location:
19p12
Exon count:
12
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (24033405..24129968)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (24014991..24312770)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene RNA, 28S ribosomal pseudogene Neighboring gene RNA, 5.8S ribosomal pseudogene 4 Neighboring gene BCL2 interacting protein 3 pseudogene 40 Neighboring gene hepatitis A virus cellular receptor 1 pseudogene 1 Neighboring gene endogenous retrovirus group K member 19 Pol protein

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

NHGRI 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.
NHGRI GWA Catalog

HIV-1 interactions

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

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ34761, FLJ34831, FLJ35501, FLJ58216

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

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_001278661.1NP_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:132
    KRAB; krueppel associated box
    COG5048
    Location:138553
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:367387
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:436460
    zf-H2C2_2; Zinc-finger double domain
  2. NM_001278662.2NP_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:132
    KRAB; krueppel associated box
    COG5048
    Location:138553
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:367387
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:436460
    zf-H2C2_2; Zinc-finger double domain
  3. NM_001278663.2NP_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
    B4E0L9, F5H2M4
    Conserved Domains (4) summary
    COG5048
    Location:94509
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:379399
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:155174
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:392416
    zf-H2C2_2; Zinc-finger double domain
  4. NM_001278664.1NP_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)
    AC092279, 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:106521
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:335355
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:404428
    zf-H2C2_2; Zinc-finger double domain
  5. NM_001278665.2NP_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:1373
    KRAB; krueppel associated box
  6. NM_001278677.2NP_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:132
    KRAB; krueppel associated box
    COG5048
    Location:138553
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:367387
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:436460
    zf-H2C2_2; Zinc-finger double domain
  7. NM_001278678.1NP_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)
    AC092279, 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:94509
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:379399
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:155174
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:392416
    zf-H2C2_2; Zinc-finger double domain
  8. NM_203282.4NP_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
    O75437
    Related
    ENSP00000349494.3, ENST00000357002.4
    Conserved Domains (3) summary
    smart00349
    Location:1373
    KRAB; krueppel associated box
    COG5048
    Location:264625
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:408428
    ZF_C2H2; C2H2 Zn finger [structural motif]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    24033405..24129968
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528443.1XP_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:132
    KRAB; krueppel associated box
    COG5048
    Location:138553
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:367387
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:436460
    zf-H2C2_2; Zinc-finger double domain
  2. XM_017027518.1XP_016883007.1  zinc finger protein 254 isoform X3

    UniProtKB/TrEMBL
    A0A087X0A2
    Conserved Domains (3) summary
    COG5048
    Location:106521
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:335355
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:404428
    zf-H2C2_2; Zinc-finger double domain
  3. XM_017027515.1XP_016883004.1  zinc finger protein 254 isoform X1

    UniProtKB/TrEMBL
    A0A087WZJ7
    Conserved Domains (4) summary
    smart00349
    Location:132
    KRAB; krueppel associated box
    COG5048
    Location:138553
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:367387
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:436460
    zf-H2C2_2; Zinc-finger double domain
  4. XM_017027519.1XP_016883008.1  zinc finger protein 254 isoform X3

    UniProtKB/TrEMBL
    A0A087X0A2
    Conserved Domains (3) summary
    COG5048
    Location:106521
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:335355
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:404428
    zf-H2C2_2; Zinc-finger double domain
  5. XM_011528444.2XP_011526746.1  zinc finger protein 254 isoform X1

    See identical proteins and their annotated locations for XP_011526746.1

    UniProtKB/TrEMBL
    A0A087WZJ7
    Conserved Domains (4) summary
    smart00349
    Location:132
    KRAB; krueppel associated box
    COG5048
    Location:138553
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:367387
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:436460
    zf-H2C2_2; Zinc-finger double domain
  6. XM_011528448.3XP_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:94509
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:379399
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:155174
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:392416
    zf-H2C2_2; Zinc-finger double domain
  7. XM_017027517.1XP_016883006.1  zinc finger protein 254 isoform X2

    Conserved Domains (3) summary
    COG5048
    Location:127542
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:412432
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:425449
    zf-H2C2_2; Zinc-finger double domain

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.
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