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    NEPRO nucleolus and neural progenitor protein [ Homo sapiens (human) ]

    Gene ID: 25871, updated on 28-Oct-2024

    Summary

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    Official Symbol
    NEPROprovided by HGNC
    Official Full Name
    nucleolus and neural progenitor proteinprovided by HGNC
    Primary source
    HGNC:HGNC:24496
    See related
    Ensembl:ENSG00000163608 MIM:617089; AllianceGenome:HGNC:24496
    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
    ANXD3; NET17; C3orf17
    Summary
    Predicted to be involved in negative regulation of neuron differentiation and positive regulation of Notch signaling pathway. Predicted to be located in nucleolus. Predicted to be active in nucleus. Implicated in anauxetic dysplasia 3. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 9.6), lymph node (RPKM 9.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NEPRO in Genome Data Viewer
    Location:
    3q13.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (113002444..113019671, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (115723401..115740627, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (112721291..112738518, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64462 Neighboring gene CD200 receptor 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:112709373-112710000 Neighboring gene GTP binding protein 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14605 Neighboring gene NEPRO antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20248 Neighboring gene DNAJB1 peudogene 2 Neighboring gene lncRNA oncogene in liver cancer 1 Neighboring gene VISTA enhancer hs1685

    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. An emerging ribosomopathy affecting the skeleton due to biallelic variations in NEPRO. Narayanan DL, et al. Am J Med Genet A, 2019 Sep. PMID 31250547
    2. Identification of Nepro, a gene required for the maintenance of neocortex neural progenitor cells downstream of Notch. Muroyama Y, et al. Development, 2009 Dec. PMID 19906856
    3. Identification and characterization of essential genes in the human genome. Wang T, et al. Science, 2015 Nov 27. PMID 26472758, Free PMC Article
    4. A comprehensive resource of interacting protein regions for refining human transcription factor networks. Miyamoto-Sato E, et al. PLoS One, 2010 Feb 24. PMID 20195357, Free PMC Article
    5. Phosphoproteome analysis of the human mitotic spindle. Nousiainen M, et al. Proc Natl Acad Sci U S A, 2006 Apr 4. PMID 16565220, Free PMC Article

    See all (43) 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

    Associated conditions

    Description Tests
    Anauxetic dysplasia 3
    MedGen: C5394289 OMIM: 618853 GeneReviews: Not available
    		Compare labs

    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

    • DKFZp434F2021

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in negative regulation of neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of Notch signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of Notch signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    nucleolus and neural progenitor protein
    Names
    protein nepro 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_001319109.2 → NP_001306038.1  nucleolus and neural progenitor protein isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two consecutive exons in the coding region compared to variant 1. The encoded isoform (d) is shorter than isoform 1.
      Source sequence(s)
      AC074044, CR749341
      Consensus CDS
      CCDS82820.1
      UniProtKB/TrEMBL
      B4DJ73
      Related
      ENSP00000373173.2, ENST00000383675.6
      Conserved Domains (1) summary
      pfam14780
      Location:12 → 118
      DUF4477; Domain of unknown function (DUF4477)

    2. NM_001319110.2 → NP_001306039.1  nucleolus and neural progenitor protein isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and 5' coding region compared to variant 1. The encoded isoform (e) is shorter than isoform a.
      Source sequence(s)
      AC074044, AK295954, CR749341
      UniProtKB/TrEMBL
      B4DJ73

    3. NM_001319111.2 → NP_001306040.1  nucleolus and neural progenitor protein isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and 5' coding region which results in the use of an alternate start codon and a frameshift compared to variant 1. The encoded isoform (f) is shorter and has a distinct N-terminus compared to isoform a
      Source sequence(s)
      AC074044, AK300811, CR749341
      UniProtKB/TrEMBL
      B4DUV5

    4. NM_001319112.2 → NP_001306041.1  nucleolus and neural progenitor protein isoform g

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR and 5' coding region which results in the use of a downstream start codon compared to variant 1. The encoded isoform (g) is shorter than isoform a.
      Source sequence(s)
      AC074044, AK295165, CR749341
      UniProtKB/TrEMBL
      B4DHL5
      Conserved Domains (1) summary
      pfam14780
      Location:1 → 91
      DUF4477; Domain of unknown function (DUF4477)

    5. NM_001319114.2 → NP_001306043.1  nucleolus and neural progenitor protein isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region which results in the use of a downstream start codon compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AC074044, AK024325, BC056663, CR749341
      UniProtKB/TrEMBL
      B4DVN9
      Conserved Domains (1) summary
      pfam14780
      Location:1 → 66
      DUF4477; Domain of unknown function (DUF4477)

    6. NM_001319115.2 → NP_001306044.1  nucleolus and neural progenitor protein isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region which results in the use of a downstream start codon compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AC074044, AL537045, BC056663, BM152568, CR749341
      UniProtKB/TrEMBL
      B4E228
      Conserved Domains (1) summary
      pfam14780
      Location:1 → 105
      DUF4477; Domain of unknown function (DUF4477)

    7. NM_015412.4 → NP_056227.2  nucleolus and neural progenitor protein isoform a

      See identical proteins and their annotated locations for NP_056227.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC074044, AL117573, BC056663, BM152568
      Consensus CDS
      CCDS33824.1
      UniProtKB/Swiss-Prot
      D3DN69, Q68DM6, Q6NW34, Q9H7U0, Q9UFM4
      UniProtKB/TrEMBL
      B4E228
      Related
      ENSP00000320251.5, ENST00000314400.10
      Conserved Domains (1) summary
      pfam14780
      Location:12 → 202
      DUF4477; Domain of unknown function (DUF4477)

    RNA

    1. NR_134969.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks multiple exons in the coding region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC074044, AK293218, CR749341

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      113002444..113019671 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047447904.1 → XP_047303860.1  nucleolus and neural progenitor protein isoform X1

    2. XM_011512638.3 → XP_011510940.1  nucleolus and neural progenitor protein isoform X3

      See identical proteins and their annotated locations for XP_011510940.1

      UniProtKB/TrEMBL
      B4DUV5

    3. XM_017006102.3 → XP_016861591.1  nucleolus and neural progenitor protein isoform X2

      Related
      ENST00000486271.5

    4. XM_047447905.1 → XP_047303861.1  nucleolus and neural progenitor protein isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      115723401..115740627 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346026.1 → XP_054202001.1  nucleolus and neural progenitor protein isoform X2

    2. XM_054346027.1 → XP_054202002.1  nucleolus and neural progenitor protein isoform X3

    3. XM_054346028.1 → XP_054202003.1  nucleolus and neural progenitor protein isoform X4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001025072.2: Suppressed sequence

      Description
      NM_001025072.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.

    2. NM_001025073.2: Suppressed sequence

      Description
      NM_001025073.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6NW34.3 GenPept UniProtKB/Swiss-Prot:Q6NW34

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