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    KLF3 KLF transcription factor 3 [ Homo sapiens (human) ]

    Gene ID: 51274, updated on 10-Dec-2024

    Summary

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    Official Symbol
    KLF3provided by HGNC
    Official Full Name
    KLF transcription factor 3provided by HGNC
    Primary source
    HGNC:HGNC:16516
    See related
    Ensembl:ENSG00000109787 MIM:609392; AllianceGenome:HGNC:16516
    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
    BKLF
    Summary
    Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in colon (RPKM 22.1), gall bladder (RPKM 19.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KLF3 in Genome Data Viewer
    Location:
    4p14
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (38664199..38701517)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (38633299..38670624)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (38665820..38703138)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1258 Neighboring gene long intergenic non-protein coding RNA 1259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21439 Neighboring gene long intergenic non-protein coding RNA 2278 Neighboring gene KLF3-I enhancer Neighboring gene KLF3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:38623749-38624601 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79844 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79852 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79860 Neighboring gene KLF3-II enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15359 Neighboring gene KLF3 promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15362 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:38668044-38668894 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:38668895-38669744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:38671391-38671960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:38674239-38674808 Neighboring gene KLF3-IIII enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15363 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79886 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21441 Neighboring gene uncharacterized LOC105374413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21442 Neighboring gene RNA, 5S ribosomal pseudogene 158

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Molecular Expression and Prognostic Implications of Krüppel-Like Factor 3 (KLF3) in Clear Cell Renal Cell Carcinoma. Wan B, et al. Crit Rev Eukaryot Gene Expr, 2024. PMID 38073441
    2. RNA sequencing analysis reveals protective role of kruppel-like factor 3 in colorectal cancer. Wang X, et al. Oncotarget, 2017 Mar 28. PMID 28423541, Free PMC Article
    3. Pan-cancer analysis of Krüppel-like factor 3 and its carcinogenesis in pancreatic cancer. Zhu J, et al. Front Immunol, 2023. PMID 37600783, Free PMC Article
    4. Expression of human Krüppel-like factor 3 in peripheral blood as a promising biomarker for acute leukemia. Yan M, et al. Cancer Med, 2020 Apr. PMID 32101374, Free PMC Article
    5. Role for SUMO modification in facilitating transcriptional repression by BKLF. Perdomo J, et al. Mol Cell Biol, 2005 Feb. PMID 15684403, Free PMC Article

    See all (54) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. microRNA-92b-3p augments colon cancer development through inhibiting KLF3.
      Title: microRNA-92b-3p augments colon cancer development through inhibiting KLF3.
    2. Molecular Expression and Prognostic Implications of Kruppel-Like Factor 3 (KLF3) in Clear Cell Renal Cell Carcinoma.
      Title: Molecular Expression and Prognostic Implications of Krüppel-Like Factor 3 (KLF3) in Clear Cell Renal Cell Carcinoma.
    3. Decreased KLF3 Expression via miR-660-5p Targeting Suppresses Gastric Cancer Cell Progression.
      Title: Decreased KLF3 Expression via miR-660-5p Targeting Suppresses Gastric Cancer Cell Progression.
    4. Pan-cancer analysis of Kruppel-like factor 3 and its carcinogenesis in pancreatic cancer.
      Title: Pan-cancer analysis of Krüppel-like factor 3 and its carcinogenesis in pancreatic cancer.
    5. KLF3 Transcription Activates WNT1 and Promotes the Growth and Metastasis of Gastric Cancer via Activation of the WNT/beta-Catenin Signaling Pathway.
      Title: KLF3 Transcription Activates WNT1 and Promotes the Growth and Metastasis of Gastric Cancer via Activation of the WNT/β-Catenin Signaling Pathway.
    6. microRNA-21-5p from M2 macrophage-derived extracellular vesicles promotes the differentiation and activity of pancreatic cancer stem cells by mediating KLF3.
      Title: microRNA-21-5p from M2 macrophage-derived extracellular vesicles promotes the differentiation and activity of pancreatic cancer stem cells by mediating KLF3.
    7. Hepatic Meteorin-like and Kruppel-like Factor 3 are Associated with Weight Loss and Liver Injury.
      Title: Hepatic Meteorin-like and Krüppel-like Factor 3 are Associated with Weight Loss and Liver Injury.
    8. Bone mesenchymal stem cells (BMSCs)-derived exosomal microRNA-21-5p regulates Kruppel-like factor 3 (KLF3) to promote osteoblast proliferation in vitro.
      Title: Bone mesenchymal stem cells (BMSCs)-derived exosomal microRNA-21-5p regulates Kruppel-like factor 3 (KLF3) to promote osteoblast proliferation in vitro.
    9. Exosome miR-23a-3p from Osteoblast Alleviates Spinal Cord Ischemia/Reperfusion Injury by Down-Regulating KLF3-Activated CCNL2 Transcription.
      Title: Exosome miR-23a-3p from Osteoblast Alleviates Spinal Cord Ischemia/Reperfusion Injury by Down-Regulating KLF3-Activated CCNL2 Transcription.
    10. Fat mass and obesity associated (FTO)-mediated N6-methyladenosine modification of Kruppel-like factor 3 (KLF3) promotes osteosarcoma progression.
      Title: Fat mass and obesity associated (FTO)-mediated N6-methyladenosine modification of Krüppel-like factor 3 (KLF3) promotes osteosarcoma progression.
    Submit: New GeneRIF Correction See all GeneRIFs (26)

    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 of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations.
    EBI GWAS Catalog
    Identification of genetic loci associated with Helicobacter pylori serologic status.
    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

    • MGC48279

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to peptide IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in hemopoiesis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    Krueppel-like factor 3
    Names
    CACCC-box-binding protein BKLF
    Kruppel like factor 3
    Kruppel-like factor 3 (basic)
    TEF-2
    basic Kruppel-like factor
    basic krueppel-like factor
    basic kruppel like factor
    transcript ch138

    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_016531.6 → NP_057615.3  Krueppel-like factor 3

      See identical proteins and their annotated locations for NP_057615.3

      Status: VALIDATED

      Source sequence(s)
      AC021860, AF285837, BU689914, DB246277
      Consensus CDS
      CCDS3444.1
      UniProtKB/Swiss-Prot
      P57682, Q6PIR1, Q86TN0, Q9P2X6
      UniProtKB/TrEMBL
      B2R8P9
      Related
      ENSP00000261438.5, ENST00000261438.10
      Conserved Domains (4) summary
      sd00017
      Location:262 → 284
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:260 → 284
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:306 → 331
      zf-H2C2_2; Zinc-finger double domain
      cd21577
      Location:49 → 260
      KLF3_N; N-terminal domain of Kruppel-like factor 3

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      38664199..38701517
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047415764.1 → XP_047271720.1  Krueppel-like factor 3 isoform X1

      UniProtKB/TrEMBL
      B2R8P9

    RNA

    1. XR_925142.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      38633299..38670624
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350158.1 → XP_054206133.1  Krueppel-like factor 3 isoform X1

      UniProtKB/TrEMBL
      B2R8P9

    RNA

    1. XR_008486992.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P57682.1 GenPept UniProtKB/Swiss-Prot:P57682

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