NME1 NME/NM23 nucleoside diphosphate kinase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NME1provided by HGNC
Official Full Name: NME/NM23 nucleoside diphosphate kinase 1provided by HGNC
Primary source: HGNC:HGNC:7849
See related: Ensembl:ENSG00000239672 MIM:156490; AllianceGenome:HGNC:7849
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NB; AWD; NBS; GAAD; NDKA; NM23; NDPKA; NDPK-A; NM23-H1
Summary: This gene (NME1) was identified because of its reduced mRNA transcript levels in highly metastatic cells. Nucleoside diphosphate kinase (NDK) exists as a hexamer composed of 'A' (encoded by this gene) and 'B' (encoded by NME2) isoforms. Mutations in this gene have been identified in aggressive neuroblastomas. Two transcript variants encoding different isoforms have been found for this gene. Co-transcription of this gene and the neighboring downstream gene (NME2) generates naturally-occurring transcripts (NME1-NME2), which encodes a fusion protein comprised of sequence sharing identity with each individual gene product. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in appendix (RPKM 37.1), brain (RPKM 32.2) and 25 other tissues See more
Orthologs: all
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Genomic context

Location:: 17q21.33

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (51153559..51162168)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (52020874..52029483)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (49230920..49239529)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

NME1 and DCC variants are associated with susceptibility and tumor characteristics in Mexican patients with colorectal cancer.
Title: NME1 and DCC variants are associated with susceptibility and tumor characteristics in Mexican patients with colorectal cancer.
NSUN6 Regulates NM23-H1 Expression in an m5C Manner to Affect Epithelial-Mesenchymal Transition in Lung Cancer.
Title: NSUN6 Regulates NM23-H1 Expression in an m5C Manner to Affect Epithelial-Mesenchymal Transition in Lung Cancer.
A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1.
Title: A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1.
Does the Blood-Brain Barrier Integrity Change in Regard to the Onset of Fetal Growth Restriction?
Title: Does the Blood-Brain Barrier Integrity Change in Regard to the Onset of Fetal Growth Restriction?
Extracellular vesicle expansion of PMIS-miR-210 expression inhibits colorectal tumour growth via apoptosis and an XIST/NME1 regulatory mechanism.
Title: Extracellular vesicle expansion of PMIS-miR-210 expression inhibits colorectal tumour growth via apoptosis and an XIST/NME1 regulatory mechanism.
Metastasis suppressor NME1 in exosomes or liposomes conveys motility and migration inhibition in breast cancer model systems.
Title: Metastasis suppressor NME1 in exosomes or liposomes conveys motility and migration inhibition in breast cancer model systems.
MicroRNA-139-5p negatively regulates NME1 expression in hepatocellular carcinoma cells.
Title: MicroRNA-139-5p negatively regulates NME1 expression in hepatocellular carcinoma cells.
Long-chain fatty acyl coenzyme A inhibits NME1/2 and regulates cancer metastasis.
Title: Long-chain fatty acyl coenzyme A inhibits NME1/2 and regulates cancer metastasis.
Metastasis-suppressor NME1 controls the invasive switch of breast cancer by regulating MT1-MMP surface clearance.
Title: Metastasis-suppressor NME1 controls the invasive switch of breast cancer by regulating MT1-MMP surface clearance.
The Potential Role of Human NME1 in Neuronal Differentiation of Porcine Mesenchymal Stem Cells: Application of NB-hNME1 as a Human NME1 Suppressor.
Title: The Potential Role of Human NME1 in Neuronal Differentiation of Porcine Mesenchymal Stem Cells: Application of NB-hNME1 as a Human NME1 Suppressor.

Submit: New GeneRIF Correction See all GeneRIFs (259)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
SiRNA-mediated knockdown of one of the components of the SET complex, NM23-H1, inhibits HIV-1 infection with significantly reduced levels of integrated HIV-1 DNA and viral production in HeLa-CD4 cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
reverse transcriptase	gag-pol	HIV-1 RT forms a complex with NDPKA in vitro	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH68986 (e-PCR)
- UniSTS:9786

D17S1989 (e-PCR)
- UniSTS:52051

GDB:196135 (e-PCR)
- UniSTS:155817

Readthrough NME1-NME2

Readthrough gene: NME1-NME2, Included gene: NME2

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3'-5' exonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA nuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables GTP binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleoside diphosphate kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables nucleoside diphosphate kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribosomal small subunit binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in CTP biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in DNA metabolic process	IEA Inferred from Electronic Annotation more info
involved_in GTP biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in UTP biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in endocytosis	IEA Inferred from Electronic Annotation more info
involved_in lactation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell population proliferation	TAS Traceable Author Statement more info	PubMed
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in phosphorylation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA binding	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of epithelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of apoptotic process	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in membrane	HDA more info	PubMed
located_in nucleus	HDA more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	TAS Traceable Author Statement more info	PubMed
located_in ruffle membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nucleoside diphosphate kinase A

Names: NDP kinase A; epididymis secretory sperm binding protein; granzyme A-activated DNase; metastasis inhibition factor nm23; non-metastatic cells 1, protein (NM23A) expressed in; tumor metastatic process-associated protein

NP_000260.1

EC 2.7.4.6

NP_937818.1

EC 2.7.4.6

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.

Genomic

NG_021169.1 RefSeqGene

Range

5001..13610

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000269.3 → NP_000260.1 nucleoside diphosphate kinase A isoform b

See identical proteins and their annotated locations for NP_000260.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1. The resulting isoform (b) has a shorter N-terminus compared to isoform a.

Source sequence(s)

AC005839, AF487339, BE727815, BF965472, BG715560, BI666785, BM479520, BU600979

Consensus CDS

CCDS11579.1

UniProtKB/Swiss-Prot

P15531, Q6FGK3, Q86XQ2, Q9UDJ6

UniProtKB/TrEMBL

A0A384MTW7

Related

ENSP00000376892.3, ENST00000393196.8

Conserved Domains (1) summary

PTZ00093
Location:5 → 151

PTZ00093; nucleoside diphosphate kinase, cytosolic; Provisional
NM_198175.1 → NP_937818.1 nucleoside diphosphate kinase A isoform a

See identical proteins and their annotated locations for NP_937818.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AF487339, AL360191, BE727815, BF965472, BG531372, BG715560, BG757842, BI666785, BM479520

Consensus CDS

CCDS11578.1

UniProtKB/Swiss-Prot

P15531

Related

ENSP00000337060.3, ENST00000336097.7

Conserved Domains (2) summary

PTZ00093
Location:30 → 176

PTZ00093; nucleoside diphosphate kinase, cytosolic; Provisional

pfam00334
Location:30 → 164

NDK; Nucleoside diphosphate kinase