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NLE1 notchless homolog 1 [ Homo sapiens (human) ]

Gene ID: 54475, updated on 2-Nov-2024

Summary

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Official Symbol
NLE1provided by HGNC
Official Full Name
notchless homolog 1provided by HGNC
Primary source
HGNC:HGNC:19889
See related
Ensembl:ENSG00000073536 MIM:620924; AllianceGenome:HGNC:19889
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
NLE; Rsa4; HUSSY7
Summary
Predicted to be involved in Notch signaling pathway and ribosomal large subunit assembly. Predicted to act upstream of or within several processes, including chordate embryonic development; hematopoietic stem cell homeostasis; and regulation of signal transduction. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 6.4), ovary (RPKM 4.9) and 25 other tissues See more
Orthologs
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Genomic context

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See NLE1 in Genome Data Viewer
Location:
17q12
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (35128730..35142303, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (36076643..36090215, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (33455749..33469322, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RAD51L3-RFFL readthrough Neighboring gene ring finger and FYVE like domain containing E3 ubiquitin protein ligase Neighboring gene ribosomal protein L37 pseudogene 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:33416287-33416938 Neighboring gene MPRA-validated peak2815 silencer Neighboring gene RNA, U6 small nuclear 840, pseudogene Neighboring gene RAD51 paralog D Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12059 Neighboring gene fibronectin type III domain containing 8 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:33468753-33469630 Neighboring gene Sharpr-MPRA regulatory region 3440/5406 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:33487621-33487791 Neighboring gene unc-45 myosin chaperone B Neighboring gene Spi-C transcription factor pseudogene 2

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 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. SMAD4 Loss Induces c-MYC-Mediated NLE1 Upregulation to Support Protein Biosynthesis, Colorectal Cancer Growth, and Metastasis. Loevenich LP, et al. Cancer Res, 2022 Dec 16. PMID 36219392, Free PMC Article
  2. The Crystal Structure of the Ubiquitin-like Domain of Ribosome Assembly Factor Ytm1 and Characterization of Its Interaction with the AAA-ATPase Midasin. Romes EM, et al. J Biol Chem, 2016 Jan 8. PMID 26601951, Free PMC Article
  3. Characterization of 16 novel human genes showing high similarity to yeast sequences. Stanchi F, et al. Yeast, 2001 Jan 15. PMID 11124703
  4. CRL4(AMBRA1) is a master regulator of D-type cyclins. Simoneschi D, et al. Nature, 2021 Apr. PMID 33854235, Free PMC Article
  5. CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Higa LA, et al. Nat Cell Biol, 2006 Nov. PMID 17041588

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SMAD4 Loss Induces c-MYC-Mediated NLE1 Upregulation to Support Protein Biosynthesis, Colorectal Cancer Growth, and Metastasis.
    Title: SMAD4 Loss Induces c-MYC-Mediated NLE1 Upregulation to Support Protein Biosynthesis, Colorectal Cancer Growth, and Metastasis.
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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10458

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in hematopoietic stem cell homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in inner cell mass cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in kidney development IEA
Inferred from Electronic Annotation
more info
  
involved_in mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of Notch signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in skeletal system morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in somitogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
notchless protein homolog 1
Names
Notchless gene homolog

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)

  1. NM_001014445.2 → NP_001014445.1  notchless protein homolog 1 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform b, which is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AB209111, BE272051, BQ070427, HY320157
    Consensus CDS
    CCDS45647.1
    UniProtKB/Swiss-Prot
    Q9NVX2
    Related
    ENSP00000466588.1, ENST00000586869.5
    Conserved Domains (3) summary
    COG2319
    Location:50 → 191
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:50 → 191
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:41 → 78
    7WD40; WD40 repeat [structural motif]

  2. NM_018096.5 → NP_060566.2  notchless protein homolog 1 isoform a

    See identical proteins and their annotated locations for NP_060566.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AC022916, BC012075, BI911995, BP244661, BQ070427, HY320157
    Consensus CDS
    CCDS11291.1
    UniProtKB/Swiss-Prot
    O60868, Q59GJ8, Q9BU54, Q9NVX2
    Related
    ENSP00000413572.3, ENST00000442241.9
    Conserved Domains (4) summary
    COG2319
    Location:107 → 485
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:106 → 484
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    pfam08154
    Location:17 → 77
    NLE; NLE (NUC135) domain
    sd00039
    Location:159 → 197
    7WD40; WD40 repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    35128730..35142303 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017024777.2 → XP_016880266.1  notchless protein homolog 1 isoform X1

    UniProtKB/Swiss-Prot
    Q9NVX2
    Conserved Domains (3) summary
    COG2319
    Location:50 → 191
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:50 → 191
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:41 → 78
    7WD40; WD40 repeat [structural motif]

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    36076643..36090215 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316529.1 → XP_054172504.1  notchless protein homolog 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NVX2.4 GenPept UniProtKB/Swiss-Prot:Q9NVX2

Gene LinkOut

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