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    PRTG protogenin [ Homo sapiens (human) ]

    Gene ID: 283659, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PRTGprovided by HGNC
    Official Full Name
    protogeninprovided by HGNC
    Primary source
    HGNC:HGNC:26373
    See related
    Ensembl:ENSG00000166450 MIM:613261; AllianceGenome:HGNC:26373
    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
    Also known as
    IGDCC5
    Summary
    This gene encodes a member of the immunoglobulin superfamily. The encoded transmembrane protein has been associated with the development of various tissues, especially neurogenesis. It has been suggested that this gene may be associated with attention deficit hyperactivity disorder (ADHD). [provided by RefSeq, Nov 2014]
    Expression
    Biased expression in thyroid (RPKM 4.7), endometrium (RPKM 1.7) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PRTG in Genome Data Viewer
    Location:
    15q21.3
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (55611544..55743152, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (53414697..53546336, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (55903742..56035350, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized mitochondrial protein AtMg00860-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6454 Neighboring gene pygopus family PHD finger 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6455 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6456 Neighboring gene uncharacterized LOC124903497 Neighboring gene NANOG hESC enhancer GRCh37_chr15:55953352-55954256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:55957303-55957803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9449 Neighboring gene NANOG hESC enhancer GRCh37_chr15:56028112-56028613 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:56034229-56035192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:56036083-56036584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:56036585-56037084 Neighboring gene NEDD4 intron nontranscribed DNase I hypersensitive site-defined enhancer Neighboring gene NEDD4 E3 ubiquitin protein ligase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40173 Neighboring gene small nucleolar RNA U13 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:56250068-56250245 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:56285058-56285840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6460 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:56286819-56287016 Neighboring gene CNOT6L 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. Nuclear translocation of intracellular domain of Protogenin by proteolytic cleavage. Watanabe Y, et al. Dev Growth Differ, 2012 Feb. PMID 22150322
    2. The novel ZEB1-upregulated protein PRTG induced by Helicobacter pylori infection promotes gastric carcinogenesis through the cGMP/PKG signaling pathway. Xiang T, et al. Cell Death Dis, 2021 Feb 4. PMID 33542225, Free PMC Article
    3. Identification of protogenin, a novel immunoglobulin superfamily gene expressed during early chick embryogenesis. Toyoda R, et al. Gene Expr Patterns, 2005 Aug. PMID 15922677
    4. Association of ADHD and the Protogenin gene in the chromosome 15q21.3 reading disabilities linkage region. Wigg KG, et al. Genes Brain Behav, 2008 Nov. PMID 19076634, Free PMC Article
    5. Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate. Leslie EJ, et al. Am J Med Genet A, 2017 Jun. PMID 28425186, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The novel ZEB1-upregulated protein PRTG induced by Helicobacter pylori infection promotes gastric carcinogenesis through the cGMP/PKG signaling pathway.
      Title: The novel ZEB1-upregulated protein PRTG induced by Helicobacter pylori infection promotes gastric carcinogenesis through the cGMP/PKG signaling pathway.
    2. We found that a burden of low-frequency coding variants in N4BP2, CDSN, PRTG, and AHRR were associated with increased risk of Nonsyndromic cleft lip with or without cleft palate (NSCL/P) . Low-frequency variants in other genes were associated with decreased risk of NSCL/P. These results demonstrate that low-frequency variants contribute to the genetic etiology of NSCL/P
      Title: Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate.
    3. PRTG is regulated by miRNA9, plays an inhibitory action on survival of chondroblasts and articular chondrocytes during chondrogenesis and osteoarthritis pathogenesis.
      Title: MicroRNA-9 regulates survival of chondroblasts and cartilage integrity by targeting protogenin.
    4. Identified association of attention deficit hyperactivity disorder (ADHD) to Protogenin (PRTG), a gene that potentially plays a role in cell migration and axon growth.
      Title: Association of ADHD and the Protogenin gene in the chromosome 15q21.3 reading disabilities linkage region.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of ADHD and the Protogenin gene in the chromosome 15q21.3 reading disabilities linkage region.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
    EBI GWAS Catalog

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12795, FLJ13221, FLJ25756

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of neurogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular space HDA PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protogenin
    Names
    immunoglobulin superfamily, DCC subclass, member 5
    protogenin homolog (Gallus gallus)
    shen-dan

    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_173814.6 → NP_776175.2  protogenin precursor

      See identical proteins and their annotated locations for NP_776175.2

      Status: REVIEWED

      Source sequence(s)
      AC009997, AC012378, AK022857, AK023283, AY630258, BQ215513, CN283887, CN352629, CN352630, CN360440, CN360445, CN369786, CN369787, CN371161, CN371162, CN371165, CN371167, DA732429, DA737881
      Consensus CDS
      CCDS42040.1
      UniProtKB/Swiss-Prot
      Q2VWP7, Q8N7D8
      Related
      ENSP00000373937.4, ENST00000389286.9
      Conserved Domains (6) summary
      smart00408
      Location:250 → 309
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:141 → 223
      IG_like; Immunoglobulin like
      cd00063
      Location:821 → 911
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:327 → 412
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:624 → 699
      fn3; Fibronectin type III domain
      cl11960
      Location:40 → 130
      Ig; Immunoglobulin domain

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      55611544..55743152 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017022081.3 → XP_016877570.1  protogenin isoform X1

    2. XM_017022082.3 → XP_016877571.1  protogenin isoform X2

    3. XM_011521460.3 → XP_011519762.1  protogenin isoform X4

      Conserved Domains (5) summary
      smart00408
      Location:250 → 309
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:141 → 223
      IG_like; Immunoglobulin like
      cd00063
      Location:419 → 512
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:327 → 412
      I-set; Immunoglobulin I-set domain
      cl11960
      Location:40 → 130
      Ig; Immunoglobulin domain

    4. XM_011521459.3 → XP_011519761.1  protogenin isoform X3

      Conserved Domains (5) summary
      smart00408
      Location:250 → 309
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:141 → 223
      IG_like; Immunoglobulin like
      cd00063
      Location:419 → 512
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:327 → 412
      I-set; Immunoglobulin I-set domain
      cl11960
      Location:40 → 130
      Ig; Immunoglobulin domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      53414697..53546336 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2VWP7.1 GenPept UniProtKB/Swiss-Prot:Q2VWP7

    Gene LinkOut

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

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