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    NLE1 notchless homolog 1 [ Homo sapiens (human) ]

    Gene ID: 54475, updated on 5-Mar-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 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
    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, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 6.4), ovary (RPKM 4.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    17q12
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (35128730..35142303, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (36076643..36090215, complement)
    105.20220307 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
    • 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 (39) 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

    Process Evidence Code Pubs
    involved_in Notch signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 ribosomal large subunit assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosomal large subunit biogenesis IEA
    Inferred from Electronic Annotation
    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_2023_10

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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