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

Gene ID: 25871, updated on 3-Apr-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, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 9.6), lymph node (RPKM 9.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3q13.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (113002444..113019671, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (115723401..115740627, complement)
105.20220307 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 (putative) 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 VISTA enhancer hs1685 Neighboring gene uncharacterized LOC124906268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:112842917-112843418

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. 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 (37) 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
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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_2023_10

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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