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    PRR16 proline rich 16 [ Homo sapiens (human) ]

    Gene ID: 51334, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PRR16provided by HGNC
    Official Full Name
    proline rich 16provided by HGNC
    Primary source
    HGNC:HGNC:29654
    See related
    Ensembl:ENSG00000184838 MIM:615931; AllianceGenome:HGNC:29654
    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
    DSC54; LARGEN
    Summary
    Involved in positive regulation of cell size and positive regulation of translation. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in endometrium (RPKM 1.3), urinary bladder (RPKM 0.9) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PRR16 in Genome Data Viewer
    Location:
    5q23.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (120464278..120794594)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (120982295..121312571)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (119799995..120023027)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:119704666-119705166 Neighboring gene RNA, U6 small nuclear 718, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:119762069-119762630 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:119762631-119763190 Neighboring gene uncharacterized LOC124901054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:119800369-119800870 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:119951767-119952361 Neighboring gene PRELI domain containing 3B pseudogene 8 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:120033273-120034058 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:120038612-120039450 Neighboring gene NANOG hESC enhancer GRCh37_chr5:120039502-120040036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:120097234-120097734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:120097735-120098235 Neighboring gene RNA, U4 small nuclear 69, pseudogene Neighboring gene Sharpr-MPRA regulatory region 293 Neighboring gene uncharacterized LOC105379147 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:120278184-120278720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:120400185-120400784 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:120442433-120442934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:120442935-120443434 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:120609330-120610529 Neighboring gene uncharacterized LOC102467226

    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. Derivation of multipotent mesenchymal precursors from human embryonic stem cells. Barberi T, et al. PLoS Med, 2005 Jun. PMID 15971941, Free PMC Article
    2. Largen: a molecular regulator of mammalian cell size control. Yamamoto K, et al. Mol Cell, 2014 Mar 20. PMID 24656129
    3. Genome-wide association studies and heritability estimates of body mass index related phenotypes in Bangladeshi adults. Scannell Bryan M, et al. PLoS One, 2014. PMID 25133637, Free PMC Article
    4. A genome-wide association study (GWAS) for bronchopulmonary dysplasia. Wang H, et al. Pediatrics, 2013 Aug. PMID 23897914, Free PMC Article
    5. Characterization and Genetic Analyses of New Genes Coding for NOD2 Interacting Proteins. Thiébaut R, et al. PLoS One, 2016. PMID 27812135, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Largen, the product of a gene PRR16, increases cell size upon overexpression in human cells.
      Title: Largen: a molecular regulator of mammalian cell size control.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study (GWAS) for bronchopulmonary dysplasia.
    EBI GWAS Catalog
    Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
    EBI GWAS Catalog
    Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC104614

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of cell size IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of cell size IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of translation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of translation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein Largen
    Names
    mesenchymal stem cell protein DSC54
    proline-rich protein 16

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001300783.2 → NP_001287712.1  protein Largen isoform 1

      See identical proteins and their annotated locations for NP_001287712.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC093301, AC113418
      Consensus CDS
      CCDS75290.1
      UniProtKB/Swiss-Prot
      D3DSZ0, Q569H4, Q8IXY1, Q9NYI5
      UniProtKB/TrEMBL
      A0A0A0MSW7
      Related
      ENSP00000385118.2, ENST00000407149.7
      Conserved Domains (2) summary
      pfam15252
      Location:53 → 304
      DUF4589; Domain of unknown function (DUF4589)
      pfam06160
      Location:25 → 68
      EzrA; Septation ring formation regulator, EzrA

    2. NM_001308087.2 → NP_001295016.1  protein Largen isoform 3

      See identical proteins and their annotated locations for NP_001295016.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus, compared to isoform 1. Both variants 3 and 4 encode isoform 3.
      Source sequence(s)
      AC093301, AC113418
      Consensus CDS
      CCDS78053.1
      UniProtKB/TrEMBL
      A0A0A0MSW7
      Conserved Domains (1) summary
      pfam15252
      Location:2 → 234
      DUF4589; Domain of unknown function (DUF4589)

    3. NM_001308088.1 → NP_001295017.1  protein Largen isoform 3

      See identical proteins and their annotated locations for NP_001295017.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus, compared to isoform 1. Both variants 3 and 4 encode isoform 3.
      Source sequence(s)
      AF242769, AI572206, BM728431
      Consensus CDS
      CCDS78053.1
      UniProtKB/TrEMBL
      A0A0A0MSW7
      Related
      ENSP00000423446.1, ENST00000505123.5
      Conserved Domains (1) summary
      pfam15252
      Location:2 → 234
      DUF4589; Domain of unknown function (DUF4589)

    4. NM_016644.3 → NP_057728.1  protein Largen isoform 2

      See identical proteins and their annotated locations for NP_057728.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an additional exon in the 5' region, and it thus differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC093301, AC104110, AC113418
      Consensus CDS
      CCDS4127.1
      UniProtKB/TrEMBL
      A0A0A0MSW7
      Related
      ENSP00000368869.2, ENST00000379551.2
      Conserved Domains (1) summary
      pfam15252
      Location:31 → 281
      DUF4589; Domain of unknown function (DUF4589)

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      120464278..120794594
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417289.1 → XP_047273245.1  protein Largen isoform X1

      UniProtKB/Swiss-Prot
      D3DSZ0, Q569H4, Q8IXY1, Q9NYI5

    2. XM_047417292.1 → XP_047273248.1  protein Largen isoform X3

    3. XM_011543452.3 → XP_011541754.1  protein Largen isoform X2

      See identical proteins and their annotated locations for XP_011541754.1

      UniProtKB/TrEMBL
      A0A0A0MSW7
      Conserved Domains (1) summary
      pfam15252
      Location:5 → 255
      DUF4589; Domain of unknown function (DUF4589)

    4. XM_047417290.1 → XP_047273246.1  protein Largen isoform X3

    5. XM_047417291.1 → XP_047273247.1  protein Largen isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      120982295..121312571
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352775.1 → XP_054208750.1  protein Largen isoform X2

    2. XM_054352776.1 → XP_054208751.1  protein Largen isoform X3

    3. XM_054352777.1 → XP_054208752.1  protein Largen isoform X3

    RNA

    1. XR_008487123.1 RNA Sequence

    2. XR_008487124.1 RNA Sequence

    3. XR_008487125.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q569H4.1 GenPept UniProtKB/Swiss-Prot:Q569H4

    Gene LinkOut

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

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