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    PKNOX1 PBX/knotted 1 homeobox 1 [ Homo sapiens (human) ]

    Gene ID: 5316, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PKNOX1provided by HGNC
    Official Full Name
    PBX/knotted 1 homeobox 1provided by HGNC
    Primary source
    HGNC:HGNC:9022
    See related
    Ensembl:ENSG00000160199 MIM:602100; AllianceGenome:HGNC:9022
    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
    PREP1; pkonx1c
    Summary
    Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in angiogenesis and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within camera-type eye development; hemopoiesis; and positive regulation of transcription by RNA polymerase II. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in testis (RPKM 8.3), thyroid (RPKM 6.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PKNOX1 in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (42974562..43033931)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (41363445..41424980)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (44394672..44454041)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905023 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44376271-44377121 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:44377122-44377972 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:44379675-44380524 Neighboring gene microRNA 5692b Neighboring gene uncharacterized LOC124905024 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:44387630-44388130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44391589-44392348 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13355 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13356 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13357 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:44395471-44396197 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44401218-44401758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44401759-44402300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44402301-44402840 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:44408954-44409120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44412569-44413092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:44482429-44482929 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44489293-44489916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44489917-44490540 Neighboring gene cystathionine beta-synthase Neighboring gene ReSE screen-validated silencer GRCh37_chr21:44500286-44500457 Neighboring gene Sharpr-MPRA regulatory region 958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44506453-44507245 Neighboring gene U2 small nuclear RNA auxiliary factor 1

    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. Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia. Bol SM, et al. PLoS One, 2012. PMID 22347417, Free PMC Article
    2. Cloning of a novel homeobox-containing gene, PKNOX1, and mapping to human chromosome 21q22.3. Chen H, et al. Genomics, 1997 Apr 15. PMID 9143494
    3. [Molecular cloning for an alternatively splicing cDNA of human PKNOX1 gene and it's expression analysis]. Ni B, et al. Yi Chuan Xue Bao, 2004 Jan. PMID 15468914
    4. PREP1 tumor suppressor protects the late-replicating DNA by controlling its replication timing and symmetry. Palmigiano A, et al. Sci Rep, 2018 Feb 16. PMID 29453404, Free PMC Article
    5. Changes in HOXB6 homeodomain protein structure and localization during human epidermal development and differentiation. Kömüves LG, et al. Dev Dyn, 2000 Aug. PMID 10906782

    See all (68) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PKNOX1 acts as a transcription factor of DHH and promotes the progression of stomach adenocarcinoma by regulating the Hedgehog signalling pathway.
      Title: PKNOX1 acts as a transcription factor of DHH and promotes the progression of stomach adenocarcinoma by regulating the Hedgehog signalling pathway.
    2. Polyunsaturated fatty acids ameliorate renal stone-induced renal tubular damage via miR-93-5p/Pknox1 axis.
      Title: Polyunsaturated fatty acids ameliorate renal stone-induced renal tubular damage via miR-93-5p/Pknox1 axis.
    3. Mapping the native interaction surfaces of PREP1 with PBX1 by cross-linking mass-spectrometry and mutagenesis.
      Title: Mapping the native interaction surfaces of PREP1 with PBX1 by cross-linking mass-spectrometry and mutagenesis.
    4. These data implicate the upregulated hepatic expression of Pknox1 in type 2 diabetes mellitus (T2DM) complicated with nonalcoholic fatty liver disease (NAFLD) may be caused by the reduced expression of miR-17 family, indicating that developing miRNA-mediated regulation strategies on Pknox1 may provide new therapeutic options for metabolic disease
      Title: MiR-17 family-mediated regulation of Pknox1 influences hepatic steatosis and insulin signaling.
    5. the replication timing of a specific fraction of the human genome is affected by PREP1 tumor suppressor
      Title: PREP1 tumor suppressor protects the late-replicating DNA by controlling its replication timing and symmetry.
    6. PREP1 modulates the cellular sensitivity to TGF-beta by inducing the small mothers against decapentaplegic homolog 3 (SMAD3) nuclear translocation.
      Title: Transcription factor PREP1 induces EMT and metastasis by controlling the TGF-β-SMAD3 pathway in non-small cell lung adenocarcinoma.
    7. High levels of MEIS1 and PREP1, and low levels of PBX4 expression were founded in samples of patients with ALL.
      Title: MEIS1, PREP1, and PBX4 are differentially expressed in acute lymphoblastic leukemia: association of MEIS1 expression with higher proliferation and chemotherapy resistance.
    8. Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia
      Title: Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia.
    9. The tumor suppressor role of Prep1 is associated with the maintenance of genomic stability.
      Title: Homeodomain transcription factor and tumor suppressor Prep1 is required to maintain genomic stability.
    10. analysis of the regulatory region of the zebrafish Prep1.1 gene and the promoter of human PREP1
      Title: Characterization of the regulatory region of the zebrafish Prep1.1 gene: analogies to the promoter of the human PREP1.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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
    Common genetic variation and performance on standardized cognitive tests.
    EBI GWAS Catalog
    Genome-wide association study of biochemical traits in Korcula Island, Croatia.
    EBI GWAS Catalog
    Genome-wide association study of selenium concentrations.
    EBI GWAS Catalog
    Whole genome association scan for genetic polymorphisms influencing information processing speed.
    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)

    Pathways from PubChem

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    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 TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables chromatin 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 T cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in angiogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in camera-type eye development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in erythrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    homeobox protein PKNOX1
    Names
    PBX/knotted homeobox 1
    Pbx regulating protein-1
    homeobox protein PREP-1
    human homeobox-containing protein

    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_001286258.2 → NP_001273187.1  homeobox protein PKNOX1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' region and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AK294794, AY196965, BP369805, CN294014
      Consensus CDS
      CCDS68211.1
      UniProtKB/TrEMBL
      B4DGV5, E7EPN6
      Related
      ENSP00000402243.2, ENST00000432907.6
      Conserved Domains (2) summary
      pfam05920
      Location:160 → 199
      Homeobox_KN; Homeobox KN domain
      pfam16493
      Location:1 → 47
      Meis_PKNOX_N; N-terminal of Homeobox Meis and PKNOX1

    2. NM_001320694.2 → NP_001307623.1  homeobox protein PKNOX1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate, in-frame splice site in the central coding region compared to variant 1. It encodes isoform 3, which is shorter than isoform 1.
      Source sequence(s)
      AA494396, AP001630, AY196965, BP369805, DR000771
      UniProtKB/TrEMBL
      Q53GN9
      Conserved Domains (2) summary
      pfam05920
      Location:276 → 315
      Homeobox_KN; Homeobox KN domain
      pfam16493
      Location:80 → 165
      Meis_PKNOX_N; N-terminal of Homeobox Meis and PKNOX1

    3. NM_004571.5 → NP_004562.2  homeobox protein PKNOX1 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AY196965, BC000735, BP369805, CN294014
      Consensus CDS
      CCDS13692.1
      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87
      Related
      ENSP00000291547.4, ENST00000291547.10
      Conserved Domains (2) summary
      pfam05920
      Location:277 → 316
      Homeobox_KN; Homeobox KN domain
      pfam16493
      Location:80 → 165
      Meis_PKNOX_N; N-terminal of Homeobox Meis and PKNOX1

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      42974562..43033931
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440826.1 → XP_047296782.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87

    2. XM_047440828.1 → XP_047296784.1  homeobox protein PKNOX1 isoform X2

      UniProtKB/TrEMBL
      Q53GN9

    3. XM_047440829.1 → XP_047296785.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87

    4. XM_047440830.1 → XP_047296786.1  homeobox protein PKNOX1 isoform X2

      UniProtKB/TrEMBL
      Q53GN9

    5. XM_047440827.1 → XP_047296783.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      41363445..41424980
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324552.1 → XP_054180527.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87

    2. XM_054324553.1 → XP_054180528.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87

    3. XM_054324555.1 → XP_054180530.1  homeobox protein PKNOX1 isoform X2

      UniProtKB/TrEMBL
      Q53GN9

    4. XM_054324556.1 → XP_054180531.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87

    5. XM_054324557.1 → XP_054180532.1  homeobox protein PKNOX1 isoform X2

      UniProtKB/TrEMBL
      Q53GN9

    6. XM_054324551.1 → XP_054180526.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87

    7. XM_054324554.1 → XP_054180529.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_197976.1: Suppressed sequence

      Description
      NM_197976.1: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P55347.3 GenPept UniProtKB/Swiss-Prot:P55347

    Gene LinkOut

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

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