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    ZBTB40 zinc finger and BTB domain containing 40 [ Homo sapiens (human) ]

    Gene ID: 9923, updated on 14-Nov-2024

    Summary

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    Official Symbol
    ZBTB40provided by HGNC
    Official Full Name
    zinc finger and BTB domain containing 40provided by HGNC
    Primary source
    HGNC:HGNC:29045
    See related
    Ensembl:ENSG00000184677 MIM:612106; AllianceGenome:HGNC:29045
    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
    ZNF923
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Involved in DNA damage response. Located in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 6.6), spleen (RPKM 6.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZBTB40 in Genome Data Viewer
    Location:
    1p36.12
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (22428909..22531154)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (22252494..22354859)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (22778344..22857647)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22651838-22652529 Neighboring gene peptidylprolyl isomerase A pseudogene 34 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22702397-22702897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22716534-22717034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22717035-22717535 Neighboring gene uncharacterized LOC105376856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22743723-22744638 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:22769377-22769994 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:22769995-22770614 Neighboring gene Sharpr-MPRA regulatory region 2075 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22778273-22778834 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:22791857-22792004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22880423-22881056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22881753-22882336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22882919-22883500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22883501-22884082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22890520-22891020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22898749-22899308 Neighboring gene EPH receptor A8 Neighboring gene Sharpr-MPRA regulatory region 15208 Neighboring gene microRNA 6127

    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. ZBTB40 is a telomere-associated protein and protects telomeres in human ALT cells. Zhou M, et al. J Biol Chem, 2023 Sep. PMID 37454741, Free PMC Article
    2. Risk Variants in or Near ZBTB40 AND NFATC1 Increase the Risk of Both IBD and Adverse Bone Health Outcomes Highlighting Common Genetic Underpinnings Across Both Diseases. Cushing KC, et al. Inflamm Bowel Dis, 2023 Jun 1. PMID 36680554, Free PMC Article
    3. Opposite associations of osteoprotegerin and ZBTB40 polymorphisms with bone mineral density of the hip in postmenopausal Taiwanese women. Chao TH, et al. J Chin Med Assoc, 2012 Jul. PMID 22824048
    4. Genetic analysis of osteoblast activity identifies Zbtb40 as a regulator of osteoblast activity and bone mass. Doolittle ML, et al. PLoS Genet, 2020 Jun. PMID 32497039, Free PMC Article
    5. Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk. Duncan EL, et al. PLoS Genet, 2011 Apr. PMID 21533022, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZBTB40 is a telomere-associated protein and protects telomeres in human ALT cells.
      Title: ZBTB40 is a telomere-associated protein and protects telomeres in human ALT cells.
    2. Risk Variants in or Near ZBTB40 AND NFATC1 Increase the Risk of Both IBD and Adverse Bone Health Outcomes Highlighting Common Genetic Underpinnings Across Both Diseases.
      Title: Risk Variants in or Near ZBTB40 AND NFATC1 Increase the Risk of Both IBD and Adverse Bone Health Outcomes Highlighting Common Genetic Underpinnings Across Both Diseases.
    3. Opposite associations of osteoprotegerin and ZBTB40 polymorphisms with bone mineral density of the hip in postmenopausal Taiwanese women.
      Title: Opposite associations of osteoprotegerin and ZBTB40 polymorphisms with bone mineral density of the hip in postmenopausal Taiwanese women.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Analysis of recently identified osteoporosis susceptibility genes in Han Chinese women.
    Submit: New GeneRIF Correction

    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
    Genome-wide association study link novel loci to endometriosis.
    EBI GWAS Catalog
    Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Multiple genetic loci for bone mineral density and fractures.
    EBI GWAS Catalog
    Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
    EBI GWAS Catalog
    Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0478, MGC133098

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific 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 
    Process Evidence Code Pubs
    involved_in DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in bone mineralization NAS
    Non-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
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    zinc finger and BTB domain-containing protein 40

    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_001083621.2 → NP_001077090.1  zinc finger and BTB domain-containing protein 40 isoform a

      See identical proteins and their annotated locations for NP_001077090.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same isoform (a).
      Source sequence(s)
      AK091019, AL035703, AL358788, BC114607, DA248977
      Consensus CDS
      CCDS224.1
      UniProtKB/Swiss-Prot
      O75066, Q5TFU5, Q8N1R1, Q9NUA8
      UniProtKB/TrEMBL
      Q1RMZ5
      Related
      ENSP00000384527.1, ENST00000404138.5
      Conserved Domains (6) summary
      smart00225
      Location:25 → 113
      BTB; Broad-Complex, Tramtrack and Bric a brac
      COG5048
      Location:794 → 970
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:838 → 858
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:952 → 970
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00651
      Location:19 → 113
      BTB; BTB/POZ domain
      pfam13465
      Location:907 → 932
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001330398.2 → NP_001317327.1  zinc finger and BTB domain-containing protein 40 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks two alternate in-frame exons compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AL035703, AL358788
      Consensus CDS
      CCDS81278.1
      UniProtKB/TrEMBL
      F8WAI8, Q1RMZ5
      Related
      ENSP00000363782.4, ENST00000374651.8
      Conserved Domains (6) summary
      COG5048
      Location:682 → 858
      COG5048; FOG: Zn-finger [General function prediction only]
      COG5189
      Location:805 → 919
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:726 → 746
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:840 → 858
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00651
      Location:19 → 113
      BTB; BTB/POZ domain
      cl28408
      Location:150 → 231
      UBQ; Ubiquitin homologues

    3. NM_014870.4 → NP_055685.3  zinc finger and BTB domain-containing protein 40 isoform a

      See identical proteins and their annotated locations for NP_055685.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (a).
      Source sequence(s)
      AL035703, BC114607, DA248977, DA787818
      Consensus CDS
      CCDS224.1
      UniProtKB/Swiss-Prot
      O75066, Q5TFU5, Q8N1R1, Q9NUA8
      UniProtKB/TrEMBL
      Q1RMZ5
      Related
      ENSP00000364798.4, ENST00000375647.5
      Conserved Domains (6) summary
      smart00225
      Location:25 → 113
      BTB; Broad-Complex, Tramtrack and Bric a brac
      COG5048
      Location:794 → 970
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:838 → 858
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:952 → 970
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00651
      Location:19 → 113
      BTB; BTB/POZ domain
      pfam13465
      Location:907 → 932
      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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      22428909..22531154
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011542499.3 → XP_011540801.1  zinc finger and BTB domain-containing protein 40 isoform X1

      See identical proteins and their annotated locations for XP_011540801.1

      UniProtKB/Swiss-Prot
      O75066, Q5TFU5, Q8N1R1, Q9NUA8
      UniProtKB/TrEMBL
      Q1RMZ5
      Conserved Domains (6) summary
      smart00225
      Location:25 → 113
      BTB; Broad-Complex, Tramtrack and Bric a brac
      COG5048
      Location:794 → 970
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:838 → 858
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:952 → 970
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00651
      Location:19 → 113
      BTB; BTB/POZ domain
      pfam13465
      Location:907 → 932
      zf-H2C2_2; Zinc-finger double domain

    2. XM_047436105.1 → XP_047292061.1  zinc finger and BTB domain-containing protein 40 isoform X2

    3. XM_011542500.3 → XP_011540802.1  zinc finger and BTB domain-containing protein 40 isoform X3

      Conserved Domains (4) summary
      COG5048
      Location:217 → 393
      COG5048; FOG: Zn-finger [General function prediction only]
      COG5189
      Location:340 → 454
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      sd00017
      Location:261 → 281
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:375 → 392
      ZF_C2H2; C2H2 Zn finger [structural motif]

    RNA

    1. XR_946804.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      22252494..22354859
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339942.1 → XP_054195917.1  zinc finger and BTB domain-containing protein 40 isoform X1

    2. XM_054339943.1 → XP_054195918.1  zinc finger and BTB domain-containing protein 40 isoform X2

    3. XM_054339944.1 → XP_054195919.1  zinc finger and BTB domain-containing protein 40 isoform X3

    RNA

    1. XR_008486221.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NUA8.4 GenPept UniProtKB/Swiss-Prot:Q9NUA8

    Gene LinkOut

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

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