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PRR16 proline rich 16 [ Homo sapiens (human) ]

Gene ID: 51334, updated on 27-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
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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
  • 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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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
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)

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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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

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