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ZNF140 zinc finger protein 140 [ Homo sapiens (human) ]

Gene ID: 7699, updated on 5-Mar-2024

Summary

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Official Symbol
ZNF140provided by HGNC
Official Full Name
zinc finger protein 140provided by HGNC
Primary source
HGNC:HGNC:12925
See related
Ensembl:ENSG00000196387 MIM:604082; AllianceGenome:HGNC:12925
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
pHZ-39
Summary
Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 3.0), testis (RPKM 2.6) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
12q24.33
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (133080425..133107428)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (133133853..133164744)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (133657509..133684014)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7397 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5134 Neighboring gene ZNF84 divergent transcript Neighboring gene PTP4A1 pseudogene 2 Neighboring gene zinc finger protein 84 Neighboring gene MPRA-validated peak2056 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7399 Neighboring gene zinc finger protein 891 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_26217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5136 Neighboring gene ribosomal protein L23a pseudogene 67 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7400 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_26228 Neighboring gene zinc finger protein 10 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:133731795-133732994

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. Characterization of the human Fc gamma RIIB gene promoter: human zinc-finger proteins (ZNF140 and ZNF91) that bind to different regions function as transcription repressors. Nishimura T, et al. Int Immunol, 2001 Aug. PMID 11470777
  2. KAP-1, a novel corepressor for the highly conserved KRAB repression domain. Friedman JR, et al. Genes Dev, 1996 Aug 15. PMID 8769649
  3. Repression of transcriptional activity by heterologous KRAB domains present in zinc finger proteins. Vissing H, et al. FEBS Lett, 1995 Aug 7. PMID 7649249
  4. Isolation and fine mapping of 16 novel human zinc finger-encoding cDNAs identify putative candidate genes for developmental and malignant disorders. Tommerup N, et al. Genomics, 1995 May 20. PMID 7557990
  5. SR protein kinases promote splicing of nonconsensus introns. Lipp JJ, et al. Nat Struct Mol Biol, 2015 Aug. PMID 26167880

See all (17) 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

Homology

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 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
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 140

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_001300776.2 → NP_001287705.1  zinc finger protein 140 isoform 2

    See identical proteins and their annotated locations for NP_001287705.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1. Variants 2 and 4 encode the same protein (isoform 2).
    Source sequence(s)
    AK303240, BC022291
    Consensus CDS
    CCDS73550.1
    UniProtKB/Swiss-Prot
    P52738
    Related
    ENSP00000445411.1, ENST00000544426.5
    Conserved Domains (3) summary
    COG5048
    Location:56 → 349
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:88 → 108
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:129 → 153
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001300777.2 → NP_001287706.1  zinc finger protein 140 isoform 3

    See identical proteins and their annotated locations for NP_001287706.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1.Transcript Variant:
    Source sequence(s)
    AK122741, AK296572, BC022291
    UniProtKB/TrEMBL
    B4DKI0
    Conserved Domains (3) summary
    COG5048
    Location:31 → 324
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:63 → 83
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:104 → 128
    zf-H2C2_2; Zinc-finger double domain

  3. NM_001300778.2 → NP_001287707.1  zinc finger protein 140 isoform 2

    See identical proteins and their annotated locations for NP_001287707.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1. Variants 2 and 4 encode the same protein (isoform 2).
    Source sequence(s)
    AK122741, BC022291
    Consensus CDS
    CCDS73550.1
    UniProtKB/Swiss-Prot
    P52738
    Conserved Domains (3) summary
    COG5048
    Location:56 → 349
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:88 → 108
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:129 → 153
    zf-H2C2_2; Zinc-finger double domain

  4. NM_003440.4 → NP_003431.2  zinc finger protein 140 isoform 1

    See identical proteins and their annotated locations for NP_003431.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK122741, BC022291
    Consensus CDS
    CCDS9282.1
    UniProtKB/Swiss-Prot
    D3DXJ3, P52738, Q05CP6, Q8IV75
    Related
    ENSP00000347755.2, ENST00000355557.7
    Conserved Domains (3) summary
    smart00349
    Location:6 → 65
    KRAB; krueppel associated box
    COG5048
    Location:159 → 452
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:191 → 211
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    133080425..133107428
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534834.4 → XP_011533136.1  zinc finger protein 140 isoform X1

    See identical proteins and their annotated locations for XP_011533136.1

    Conserved Domains (5) summary
    smart00349
    Location:6 → 66
    KRAB; krueppel associated box
    COG5048
    Location:160 → 453
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:192 → 212
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:6 → 45
    KRAB; KRAB box
    pfam13465
    Location:233 → 257
    zf-H2C2_2; Zinc-finger double domain

  2. XM_011534835.4 → XP_011533137.1  zinc finger protein 140 isoform X2

    See identical proteins and their annotated locations for XP_011533137.1

    UniProtKB/Swiss-Prot
    D3DXJ3, P52738, Q05CP6, Q8IV75
    Conserved Domains (3) summary
    smart00349
    Location:6 → 65
    KRAB; krueppel associated box
    COG5048
    Location:159 → 452
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:191 → 211
    ZF_C2H2; C2H2 Zn finger [structural motif]

  3. XM_011534833.3 → XP_011533135.1  zinc finger protein 140 isoform X1

    See identical proteins and their annotated locations for XP_011533135.1

    Conserved Domains (5) summary
    smart00349
    Location:6 → 66
    KRAB; krueppel associated box
    COG5048
    Location:160 → 453
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:192 → 212
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:6 → 45
    KRAB; KRAB box
    pfam13465
    Location:233 → 257
    zf-H2C2_2; Zinc-finger double domain

  4. XM_011534837.3 → XP_011533139.1  zinc finger protein 140 isoform X3

    See identical proteins and their annotated locations for XP_011533139.1

    Conserved Domains (3) summary
    COG5048
    Location:126 → 419
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:158 → 178
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:199 → 223
    zf-H2C2_2; Zinc-finger double domain

  5. XM_047429512.1 → XP_047285468.1  zinc finger protein 140 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    133133853..133164744
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373144.1 → XP_054229119.1  zinc finger protein 140 isoform X1

  2. XM_054373146.1 → XP_054229121.1  zinc finger protein 140 isoform X2

    UniProtKB/Swiss-Prot
    D3DXJ3, P52738, Q05CP6, Q8IV75

  3. XM_054373145.1 → XP_054229120.1  zinc finger protein 140 isoform X1

  4. XM_054373147.1 → XP_054229122.1  zinc finger protein 140 isoform X2

    UniProtKB/Swiss-Prot
    D3DXJ3, P52738, Q05CP6, Q8IV75

  5. XM_054373148.1 → XP_054229123.1  zinc finger protein 140 isoform X3

  6. XM_054373149.1 → XP_054229124.1  zinc finger protein 140 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P52738.2 GenPept UniProtKB/Swiss-Prot:P52738

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