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    NHLRC3 NHL repeat containing 3 [ Homo sapiens (human) ]

    Gene ID: 387921, updated on 14-Nov-2024

    Summary

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    Official Symbol
    NHLRC3provided by HGNC
    Official Full Name
    NHL repeat containing 3provided by HGNC
    Primary source
    HGNC:HGNC:33751
    See related
    Ensembl:ENSG00000188811 AllianceGenome:HGNC:33751
    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
    Summary
    This gene encodes a protein containing NCL-1, HT2A and Lin-41 (NHL) family repeats. Mammalian NHL-repeat containing proteins may be involved in a variety of enzymatic processes, including protein modification through ubiquitination. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Aug 2012]
    Expression
    Ubiquitous expression in thyroid (RPKM 11.4), fat (RPKM 10.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NHLRC3 in Genome Data Viewer
    Location:
    13q13.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (39038311..39050109)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (38257954..38269752)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (39612448..39624246)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene stomatin like 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:39580698-39581306 Neighboring gene Sharpr-MPRA regulatory region 13170 Neighboring gene proline and serine rich 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7597 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5275 Neighboring gene uncharacterized LOC105370169 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:39704423-39704944 Neighboring gene nuclear transport factor 2 like export factor 1 pseudogene 1

    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. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. Prunotto M, et al. J Proteomics, 2013 Apr 26. PMID 23376485
    2. OpenCell: Endogenous tagging for the cartography of human cellular organization. Cho NH, et al. Science, 2022 Mar 11. PMID 35271311, Free PMC Article
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
    4. The BioPlex Network: A Systematic Exploration of the Human Interactome. Huttlin EL, et al. Cell, 2015 Jul 16. PMID 26186194, Free PMC Article
    5. Architecture of the human interactome defines protein communities and disease networks. Huttlin EL, et al. Nature, 2017 May 25. PMID 28514442, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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

    Homology

    Clone Names

    • DKFZp313M1221, DKFZp686E1140

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in azurophil granule lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    NHL repeat-containing protein 3

    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_001012754.4 → NP_001012772.1  NHL repeat-containing protein 3 isoform a precursor

      See identical proteins and their annotated locations for NP_001012772.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AL445590, BC140877, CR749318
      Consensus CDS
      CCDS31961.1
      UniProtKB/Swiss-Prot
      B2RTZ2, B4DTL0, Q5JS37, Q69YI9
      UniProtKB/TrEMBL
      B4DRC8
      Related
      ENSP00000368920.3, ENST00000379600.8
      Conserved Domains (2) summary
      cd05819
      Location:107 → 153
      NHL; NHL repeat [structural motif]
      cl18310
      Location:66 → 336
      NHL; NHL repeat unit of beta-propeller proteins

    2. NM_001017370.3 → NP_001017370.1  NHL repeat-containing protein 3 isoform b

      See identical proteins and their annotated locations for NP_001017370.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AL445590, BC140877, BX647872, CR749318
      Consensus CDS
      CCDS31962.1
      UniProtKB/TrEMBL
      B4DRC8
      Related
      ENSP00000368919.2, ENST00000379599.6
      Conserved Domains (2) summary
      cd05819
      Location:66 → 138
      NHL; NHL repeat [structural motif]
      cl18310
      Location:61 → 269
      NHL; NHL repeat unit of beta-propeller proteins

    RNA

    1. NR_073109.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site at the 5' end, compared to variant 1. This variant is represented as non-coding because it lacks a portion of the coding region, including the translational start codon, found in variant 1.
      Source sequence(s)
      AL445590, BC052492, BC140877, CR749318, DA772703
      Related
      ENST00000470258.5

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      39038311..39050109
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      38257954..38269752
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5JS37.1 GenPept UniProtKB/Swiss-Prot:Q5JS37

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
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    Tools
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