NOL9 nucleolar protein 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NOL9provided by HGNC
Official Full Name: nucleolar protein 9provided by HGNC
Primary source: HGNC:HGNC:26265
See related: Ensembl:ENSG00000162408 MIM:620304; AllianceGenome:HGNC:26265
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: Grc3; NET6
Summary: Enables polynucleotide 5'-hydroxyl-kinase activity. Involved in maturation of 5.8S rRNA. Located in intermediate filament cytoskeleton and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in spleen (RPKM 3.0), bone marrow (RPKM 2.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.31

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (6521347..6554513, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (6046991..6080171, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (6581407..6614573, complement)

Chromosome 1 - NC_000001.11 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?

a Nol9-encoded nucleolar localization sequence that is responsible for nucleolar transport of the assembled Las1L-Nol9 complex, is reported.
Title: Nol9 Is a Spatial Regulator for the Human ITS2 Pre-rRNA Endonuclease-Kinase Complex.
we present the nol9sa1022/sa1022 mutant, a novel zebrafish ribosomopathy model, which recapitulates key human disease characteristics.
Title: The Ribosome Biogenesis Protein Nol9 Is Essential for Definitive Hematopoiesis and Pancreas Morphogenesis in Zebrafish.
The polynucleotide kinase activity of Nol9 is required for efficient generation of the 5.8S and 28S ribosomal RNAs from the 32S precursor.
Title: Nol9 is a novel polynucleotide 5'-kinase involved in ribosomal RNA processing.

Submit: New GeneRIF Correction

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10S275 (e-PCR)
- UniSTS:147992

GDB:312794 (e-PCR)
- UniSTS:30247

L17705 (e-PCR)
- UniSTS:66091

PMC156606P2 (e-PCR)
- UniSTS:271409

D8S2279 (e-PCR)
- UniSTS:473907

RH68223 (e-PCR)
- UniSTS:56125

SHGC-63524 (e-PCR)
- UniSTS:73791

L17796 (e-PCR)
- UniSTS:12896

D10S16 (e-PCR)
- UniSTS:155756

D15S1477 (e-PCR)
- UniSTS:474482

L17809 (e-PCR)
- UniSTS:39087

L17971 (e-PCR)
- UniSTS:43966

A006V30 (e-PCR)
- UniSTS:45264

GDB:631802 (e-PCR)
- UniSTS:158429

D3S1673 (e-PCR)
- UniSTS:148450

D22S958 (e-PCR)
- UniSTS:259319

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	TAS Traceable Author Statement more info	PubMed
enables ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables polynucleotide 5'-hydroxyl-kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IBA Inferred from Biological aspect of Ancestor more info
involved_in maturation of 5.8S rRNA	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in intermediate filament cytoskeleton	IDA Inferred from Direct Assay more info
located_in membrane	HDA more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	TAS Traceable Author Statement more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: polynucleotide 5'-hydroxyl-kinase NOL9

Names: polynucleotide 5'-kinase

NP_078930.4

EC 2.7.1.78

XP_005263550.1

EC 2.7.1.78

XP_011540449.1

EC 2.7.1.78

XP_047286512.1

EC 2.7.1.78

XP_047286521.1

EC 2.7.1.78

XP_054194723.1

EC 2.7.1.78

XP_054194724.1

EC 2.7.1.78

XP_054194725.1

EC 2.7.1.78

XP_054194726.1

EC 2.7.1.78

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_024654.5 → NP_078930.4 polynucleotide 5'-hydroxyl-kinase NOL9

Status: VALIDATED

Source sequence(s)

AL591866

Consensus CDS

CCDS80.1

UniProtKB/Swiss-Prot

Q2NL84, Q4VBY3, Q5SY16, Q6P472, Q7L4D6, Q96EE0, Q9H5L4

Related

ENSP00000366934.5, ENST00000377705.6

Conserved Domains (1) summary

pfam16575
Location:306 → 415

CLP1_P; mRNA cleavage and polyadenylation factor CLP1 P-loop

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_000001.11 Reference GRCh38.p14 Primary Assembly

Range

6521347..6554513 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047430565.1 → XP_047286521.1 polynucleotide 5'-hydroxyl-kinase NOL9 isoform X2
XM_005263493.5 → XP_005263550.1 polynucleotide 5'-hydroxyl-kinase NOL9 isoform X1

Conserved Domains (1) summary

pfam16575
Location:19 → 128

CLP1_P; mRNA cleavage and polyadenylation factor CLP1 P-loop
XM_047430556.1 → XP_047286512.1 polynucleotide 5'-hydroxyl-kinase NOL9 isoform X2
XM_011542147.4 → XP_011540449.1 polynucleotide 5'-hydroxyl-kinase NOL9 isoform X2

See identical proteins and their annotated locations for XP_011540449.1

UniProtKB/Swiss-Prot

Q5SY16

Conserved Domains (1) summary

cl38936
Location:3 → 45

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

6046991..6080171 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054338750.1 → XP_054194725.1 polynucleotide 5'-hydroxyl-kinase NOL9 isoform X2
XM_054338748.1 → XP_054194723.1 polynucleotide 5'-hydroxyl-kinase NOL9 isoform X1
XM_054338749.1 → XP_054194724.1 polynucleotide 5'-hydroxyl-kinase NOL9 isoform X2
XM_054338751.1 → XP_054194726.1 polynucleotide 5'-hydroxyl-kinase NOL9 isoform X2