Human Gene P3H1 (uc001chv.2)
  Description: Homo sapiens leucine proline-enriched proteoglycan (leprecan) 1 (P3H1), transcript variant 1, mRNA.
RefSeq Summary (NM_022356): This gene encodes an enzyme that is a member of the collagen prolyl hydroxylase family. These enzymes are localized to the endoplasmic reticulum and their activity is required for proper collagen synthesis and assembly. Mutations in this gene are associated with osteogenesis imperfecta type VIII. Three alternatively spliced transcript variants encoding different isoforms have been described. Other variants may exist, but their biological validity has not been determined. [provided by RefSeq, Aug 2011].
Transcript (Including UTRs)
   Position: hg19 chr1:43,212,006-43,232,755 Size: 20,750 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr1:43,212,368-43,232,642 Size: 20,275 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:43,212,006-43,232,755)mRNA (may differ from genome)Protein (736 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: P3H1_HUMAN
DESCRIPTION: RecName: Full=Prolyl 3-hydroxylase 1; EC=1.14.11.7; AltName: Full=Growth suppressor 1; AltName: Full=Leucine- and proline-enriched proteoglycan 1; Short=Leprecan-1; Flags: Precursor;
FUNCTION: Basement membrane-associated chondroitin sulfate proteoglycan (CSPG). Has prolyl 3-hydroxylase activity catalyzing the post-translational formation of 3-hydroxyproline in -Xaa-Pro- Gly- sequences in collagens, especially types IV and V. May be involved in the secretory pathway of cells. Has growth suppressive activity in fibroblasts.
CATALYTIC ACTIVITY: L-proline-[procollagen] + 2-oxoglutarate + O(2) = trans-3-hydroxy-L-proline-[procollagen] + succinate + CO(2).
COFACTOR: Iron (By similarity).
COFACTOR: Ascorbate (By similarity).
SUBCELLULAR LOCATION: Endoplasmic reticulum (By similarity). Secreted, extracellular space, extracellular matrix (By similarity). Note=Secreted into the extracellular matrix as a chondroitin sulfate proteoglycan (CSPG).
PTM: O-glycosylated; chondroitin sulfate (By similarity).
DISEASE: Defects in LEPRE1 are the cause of osteogenesis imperfecta type 8 (OI8) [MIM:610915]. A connective tissue disorder characterized by disproportionate short stature, severe osteoporosis, shortening of the long bones, white sclerae, a round face and a short barrel-shaped chest.
SIMILARITY: Belongs to the leprecan family.
SIMILARITY: Contains 1 Fe2OG dioxygenase domain.
SIMILARITY: Contains 4 TPR repeats.
SEQUENCE CAUTION: Sequence=AAH15309.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAI08312.1; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=BAB15256.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/LEPRE1";
WEB RESOURCE: Name=Osteogenesis imperfecta variant database; Note=Prolyl 3-hydroxylase 1 (LEPRE1); URL="http://oi.gene.le.ac.uk/home.php?select_db=LEPRE1";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: P3H1
Diseases sorted by gene-association score: osteogenesis imperfecta, type viii* (1027), osteogenesis imperfecta, type ii* (215), p3h1-related osteogenesis imperfecta* (200), osteogenesis imperfecta, type iii* (132), osteogenesis imperfecta (35), dentinogenesis imperfecta (9), cervical incompetence (8), bruck syndrome (6), bone development disease (5), connective tissue disease (2)
* = Manually curated disease association

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 33.05 RPKM in Cells - Cultured fibroblasts
Total median expression: 531.16 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -59.60113-0.527 Picture PostScript Text
3' UTR -132.60362-0.366 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005123 - Oxoglu/Fe-dep_dioxygenase
IPR006620 - Pro_4_hyd_alph
IPR011990 - TPR-like_helical

Pfam Domains:
PF03171 - 2OG-Fe(II) oxygenase superfamily
PF13640 - 2OG-Fe(II) oxygenase superfamily

SCOP Domains:
81901 - HCP-like
48452 - TPR-like

ModBase Predicted Comparative 3D Structure on Q32P28
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0005506 iron ion binding
GO:0016491 oxidoreductase activity
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0019797 procollagen-proline 3-dioxygenase activity
GO:0031418 L-ascorbic acid binding
GO:0044877 macromolecular complex binding
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
GO:0005518 collagen binding

Biological Process:
GO:0006457 protein folding
GO:0008285 negative regulation of cell proliferation
GO:0010976 positive regulation of neuron projection development
GO:0018126 protein hydroxylation
GO:0019511 peptidyl-proline hydroxylation
GO:0032963 collagen metabolic process
GO:0050708 regulation of protein secretion
GO:0050821 protein stabilization
GO:0055114 oxidation-reduction process
GO:0060348 bone development
GO:0061077 chaperone-mediated protein folding
GO:1901874 negative regulation of post-translational protein modification

Cellular Component:
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0016020 membrane
GO:0032991 macromolecular complex
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF206593 - JP 2014500723-A/14096: Polycomb-Associated Non-Coding RNAs.
LF356423 - JP 2014500723-A/163926: Polycomb-Associated Non-Coding RNAs.
CR749690 - Homo sapiens mRNA; cDNA DKFZp547C166 (from clone DKFZp547C166).
AK025841 - Homo sapiens cDNA: FLJ22188 fis, clone HRC01030.
BC051324 - Homo sapiens leucine proline-enriched proteoglycan (leprecan) 1, mRNA (cDNA clone IMAGE:6270659), **** WARNING: chimeric clone ****.
BC064992 - Homo sapiens cDNA clone IMAGE:5798179, **** WARNING: chimeric clone ****.
BC091513 - Homo sapiens leucine proline-enriched proteoglycan (leprecan) 1, mRNA (cDNA clone IMAGE:6187572), with apparent retained intron.
BC004160 - Homo sapiens leucine proline-enriched proteoglycan (leprecan) 1, mRNA (cDNA clone IMAGE:2824480), containing frame-shift errors.
BC011666 - Homo sapiens cDNA clone IMAGE:4122527, **** WARNING: chimeric clone ****.
AF097431 - Homo sapiens GROS1-S protein mRNA, complete cds.
AF097432 - Homo sapiens GROS1-L protein mRNA, complete cds.
BC108311 - Homo sapiens leucine proline-enriched proteoglycan (leprecan) 1, mRNA (cDNA clone MGC:117314 IMAGE:4521167), complete cds.
AK297980 - Homo sapiens cDNA FLJ53395 complete cds, highly similar to Prolyl 3-hydroxylase 1 precursor (EC 1.14.11.7).
AK075418 - Homo sapiens cDNA PSEC0109 fis, clone NT2RP2005671, highly similar to Leucine proline-enriched proteoglycan (leprecan) 1.
AK027648 - Homo sapiens cDNA FLJ14742 fis, clone NT2RP3002650, highly similar to Mus musculus growth suppressor 1L (Gros1) mRNA.
AK027697 - Homo sapiens cDNA FLJ14791 fis, clone NT2RP4001064, weakly similar to SYNAPTONEMAL COMPLEX PROTEIN SC65.
AK027680 - Homo sapiens cDNA FLJ14774 fis, clone NT2RP4000051, weakly similar to SYNAPTONEMAL COMPLEX PROTEIN SC65.
JD209978 - Sequence 191002 from Patent EP1572962.
JD239266 - Sequence 220290 from Patent EP1572962.
JD423474 - Sequence 404498 from Patent EP1572962.
JD459438 - Sequence 440462 from Patent EP1572962.
JD159145 - Sequence 140169 from Patent EP1572962.
JD444558 - Sequence 425582 from Patent EP1572962.
JD154030 - Sequence 135054 from Patent EP1572962.
JD326108 - Sequence 307132 from Patent EP1572962.
JD435587 - Sequence 416611 from Patent EP1572962.
JD444997 - Sequence 426021 from Patent EP1572962.
JD119588 - Sequence 100612 from Patent EP1572962.
JD207369 - Sequence 188393 from Patent EP1572962.
LF356422 - JP 2014500723-A/163925: Polycomb-Associated Non-Coding RNAs.
BT007039 - Homo sapiens leucine proline-enriched proteoglycan (leprecan) 1 mRNA, complete cds.
JD155602 - Sequence 136626 from Patent EP1572962.
JD487714 - Sequence 468738 from Patent EP1572962.
JD182823 - Sequence 163847 from Patent EP1572962.
JD236203 - Sequence 217227 from Patent EP1572962.
KJ894540 - Synthetic construct Homo sapiens clone ccsbBroadEn_03934 LEPRE1 gene, encodes complete protein.
BC143962 - Homo sapiens cDNA clone IMAGE:9052480, with apparent retained intron.
BC143961 - Homo sapiens cDNA clone IMAGE:9052479.
LF356421 - JP 2014500723-A/163924: Polycomb-Associated Non-Coding RNAs.
LF356419 - JP 2014500723-A/163922: Polycomb-Associated Non-Coding RNAs.
LF356417 - JP 2014500723-A/163920: Polycomb-Associated Non-Coding RNAs.
LF356416 - JP 2014500723-A/163919: Polycomb-Associated Non-Coding RNAs.
AK300210 - Homo sapiens cDNA FLJ54152 complete cds, highly similar to Prolyl 3-hydroxylase 1 precursor (EC 1.14.11.7).
LF356415 - JP 2014500723-A/163918: Polycomb-Associated Non-Coding RNAs.
LF213504 - JP 2014500723-A/21007: Polycomb-Associated Non-Coding RNAs.
BC068461 - Homo sapiens leucine proline-enriched proteoglycan (leprecan) 1, mRNA (cDNA clone IMAGE:30342539), with apparent retained intron.
LF356413 - JP 2014500723-A/163916: Polycomb-Associated Non-Coding RNAs.
LF356412 - JP 2014500723-A/163915: Polycomb-Associated Non-Coding RNAs.
LF356410 - JP 2014500723-A/163913: Polycomb-Associated Non-Coding RNAs.
LF356409 - JP 2014500723-A/163912: Polycomb-Associated Non-Coding RNAs.
LF356408 - JP 2014500723-A/163911: Polycomb-Associated Non-Coding RNAs.
MA442170 - JP 2018138019-A/14096: Polycomb-Associated Non-Coding RNAs.
MA592000 - JP 2018138019-A/163926: Polycomb-Associated Non-Coding RNAs.
MA591999 - JP 2018138019-A/163925: Polycomb-Associated Non-Coding RNAs.
MA591998 - JP 2018138019-A/163924: Polycomb-Associated Non-Coding RNAs.
MA591996 - JP 2018138019-A/163922: Polycomb-Associated Non-Coding RNAs.
MA591994 - JP 2018138019-A/163920: Polycomb-Associated Non-Coding RNAs.
MA591993 - JP 2018138019-A/163919: Polycomb-Associated Non-Coding RNAs.
MA591992 - JP 2018138019-A/163918: Polycomb-Associated Non-Coding RNAs.
MA449081 - JP 2018138019-A/21007: Polycomb-Associated Non-Coding RNAs.
MA591990 - JP 2018138019-A/163916: Polycomb-Associated Non-Coding RNAs.
MA591989 - JP 2018138019-A/163915: Polycomb-Associated Non-Coding RNAs.
MA591987 - JP 2018138019-A/163913: Polycomb-Associated Non-Coding RNAs.
MA591986 - JP 2018138019-A/163912: Polycomb-Associated Non-Coding RNAs.
MA591985 - JP 2018138019-A/163911: Polycomb-Associated Non-Coding RNAs.
BC015309 - Homo sapiens leucine proline-enriched proteoglycan (leprecan) 1, mRNA (cDNA clone IMAGE:4395073), partial cds.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q32P28 (Reactome details) participates in the following event(s):

R-HSA-2022073 Procollagen triple helix formation
R-HSA-8948230 P3HB binds 4-Hyp-collagen propeptides
R-HSA-1980233 Collagen prolyl 3-hydroxylase converts 4-Hyp collagen to 3,4-Hyp collagen
R-HSA-1650814 Collagen biosynthesis and modifying enzymes
R-HSA-1474290 Collagen formation
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: GROS1, LEPRE1, NM_022356, NP_071751, P3H1_HUMAN, PSEC0109, Q32P28, Q7KZR4, Q96BR8, Q96SK8, Q96SL5, Q96SN3, Q9H6K3, Q9HC86, Q9HC87
UCSC ID: uc001chv.2
RefSeq Accession: NM_022356
Protein: Q32P28 (aka P3H1_HUMAN)
CCDS: CCDS472.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_022356.3
exon count: 15CDS single in 3' UTR: no RNA size: 2696
ORF size: 2211CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 4592.00frame shift in genome: no % Coverage: 99.63
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.