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

Gene ID: 387921, updated on 27-Aug-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
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Genomic context

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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)
105.20220307 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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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

Homology

Clone Names

  • DKFZp313M1221, DKFZp686E1140

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables translation repressor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in negative regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
  
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

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