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

    Gene ID: 5316, updated on 17-Jun-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    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
     
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    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)

    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_001286258.2NP_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:160199
      Homeobox_KN; Homeobox KN domain
      pfam16493
      Location:147
      Meis_PKNOX_N; N-terminal of Homeobox Meis and PKNOX1
    2. NM_001320694.2NP_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:276315
      Homeobox_KN; Homeobox KN domain
      pfam16493
      Location:80165
      Meis_PKNOX_N; N-terminal of Homeobox Meis and PKNOX1
    3. NM_004571.5NP_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:277316
      Homeobox_KN; Homeobox KN domain
      pfam16493
      Location:80165
      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_047440826.1XP_047296782.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87
    2. XM_047440828.1XP_047296784.1  homeobox protein PKNOX1 isoform X2

      UniProtKB/TrEMBL
      Q53GN9
    3. XM_047440829.1XP_047296785.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87
    4. XM_047440830.1XP_047296786.1  homeobox protein PKNOX1 isoform X2

      UniProtKB/TrEMBL
      Q53GN9
    5. XM_047440827.1XP_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_054324552.1XP_054180527.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87
    2. XM_054324553.1XP_054180528.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87
    3. XM_054324555.1XP_054180530.1  homeobox protein PKNOX1 isoform X2

      UniProtKB/TrEMBL
      Q53GN9
    4. XM_054324556.1XP_054180531.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87
    5. XM_054324557.1XP_054180532.1  homeobox protein PKNOX1 isoform X2

      UniProtKB/TrEMBL
      Q53GN9
    6. XM_054324551.1XP_054180526.1  homeobox protein PKNOX1 isoform X1

      UniProtKB/Swiss-Prot
      O00528, P55347, Q8IWT7
      UniProtKB/TrEMBL
      Q53GN9, Q96I87
    7. XM_054324554.1XP_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 info@ncbi.nlm.nih.gov for further information.