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

Gene ID: 5316, updated on 11-Apr-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. Predicted to be located in cytoplasm and nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 8.3), thyroid (RPKM 6.8) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (42974562..43033931)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (41363445..41424980)
105.20220307 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: 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. 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
  2. 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
  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. 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
  5. Polyunsaturated fatty acids ameliorate renal stone-induced renal tubular damage via miR-93-5p/Pknox1 axis. Liu Q, et al. Nutrition, 2023 Jan. PMID 36356379

See all (66) 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)

Genotypes

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 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 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 regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus 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

    See identical proteins and their annotated locations for NP_001273187.1

    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

    See identical proteins and their annotated locations for NP_004562.2

    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_2023_10

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
    Q96I87

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    UniProtKB/Swiss-Prot
    O00528, P55347, Q8IWT7
    UniProtKB/TrEMBL
    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 info@ncbi.nlm.nih.gov 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

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