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

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: mouse all
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Genomic context

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_000021.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Genome-wide association study of biochemical traits in Korcula Island, Croatia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of selenium concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Whole genome association scan for genetic polymorphisms influencing information processing speed. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

D21S1938 (e-PCR)
- UniSTS:21289

PKNOX1_2194 (e-PCR)
- UniSTS:280911

G48510 (e-PCR)
- UniSTS:95570

G48511 (e-PCR)
- UniSTS:95571

D17S610 (e-PCR)
- UniSTS:46230

WI-16888 (e-PCR)
- UniSTS:56495

SHGC-52028 (e-PCR)
- UniSTS:4030

STS-T84037 (e-PCR)
- UniSTS:80586

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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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)

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
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
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

NC_000021.9 Reference GRCh38.p14 Primary Assembly

Range

42974562..43033931

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

O00528, P55347, Q8IWT7

UniProtKB/TrEMBL

Q96I87
XM_047440828.1 → XP_047296784.1 homeobox protein PKNOX1 isoform X2
XM_047440829.1 → XP_047296785.1 homeobox protein PKNOX1 isoform X1

UniProtKB/Swiss-Prot

O00528, P55347, Q8IWT7

UniProtKB/TrEMBL

Q96I87
XM_047440830.1 → XP_047296786.1 homeobox protein PKNOX1 isoform X2
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

NC_060945.1 Alternate T2T-CHM13v2.0

Range

41363445..41424980

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

O00528, P55347, Q8IWT7

UniProtKB/TrEMBL

Q96I87
XM_054324553.1 → XP_054180528.1 homeobox protein PKNOX1 isoform X1

UniProtKB/Swiss-Prot

O00528, P55347, Q8IWT7

UniProtKB/TrEMBL

Q96I87
XM_054324555.1 → XP_054180530.1 homeobox protein PKNOX1 isoform X2
XM_054324556.1 → XP_054180531.1 homeobox protein PKNOX1 isoform X1

UniProtKB/Swiss-Prot

O00528, P55347, Q8IWT7

UniProtKB/TrEMBL

Q96I87
XM_054324557.1 → XP_054180532.1 homeobox protein PKNOX1 isoform X2
XM_054324551.1 → XP_054180526.1 homeobox protein PKNOX1 isoform X1

UniProtKB/Swiss-Prot

O00528, P55347, Q8IWT7

UniProtKB/TrEMBL

Q96I87
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

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.