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PLOD2 Gene

protein-coding   GIFtS: 60

GC03M143165
procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2
(Previous names: procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Products    

Aliases &
Descriptions
for PLOD2 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section
Aliases & Descriptions
procollagen-lysine, 2-oxoglutarate 5-dioxygenase 21 2     lysine hydroxylase 22
Lysyl hydroxylase 22 3     procollagen-lysine,2-oxoglutarate 5-dioxygenase 22
LH22 3     telopeptide lysyl hydroxylase2
procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 21     TLH2
OTTHUMP000002152062     EC 1.14.11.43

External Ids:    HGNC: 90821   Entrez Gene: 53522   Ensembl: ENSG000001529527   UniProtKB: O004693   

Export aliases for PLOD2 gene to outside databases

Previous GC identifers: GC03M142579 GC03M146646 GC03M147068 GC03M147109 GC03M147110 GC03M147269 GC03M145787


Summaries
for PLOD2 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for PLOD2:
The protein encoded by this gene is a membrane-bound homodimeric enzyme that is localized to the cisternae of the rough
endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in
collagen-like peptides. The resultant hydroxylysyl groups are attachment sites for carbohydrates in collagen and thus
are critical for the stability of intermolecular crosslinks. Some patients with Ehlers-Danlos syndrome type VIB have
deficiencies in lysyl hydroxylase activity. Mutations in the coding region of this gene are associated with Bruck
syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. (provided by
RefSeq)

UniProtKB/Swiss-Prot: PLOD2_HUMAN, O00469
Function: Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of
attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links


Genomic Views
for PLOD2 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PLOD2 gene promoter:
         NF-E2   NF-E2 p45   Hlf   Bach1   Bach2   FOXJ2 (long isoform)   PPAR-gamma1   PPAR-gamma2   AREB6   c-Fos   
         Other transcription factors

   Search SABiosciences Chromatin IP Primers for PLOD2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for PLOD2 


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q24   Ensembl cytogenetic band:  3q24   HGNC cytogenetic band: 3q24

PLOD2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PLOD2 gene location

GeneLoc gene densities for chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M143165:  view genomic region     (about GC identifiers)

Start:
 143,164,166 bp from pter
End:
 143,256,088 bp from pter
Size:
 91,923 bases
Orientation:
 minus strand

1 alternative location:
Chr3- 145,787,227-145,881,440     
RefSeq DNA sequence:
NC_000003.11  NT_005612.16  

Proteins
for PLOD2 gene

(According to 1UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
About This Section
UniProtKB/Swiss-Prot: PLOD2_HUMAN, O00469 (See protein sequence)
Recommended Name: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 precursor  
Size: 737 amino acids; 84686 Da
Cofactor: Iron (By similarity)
Cofactor: Ascorbate (By similarity)
Subunit: Homodimer (By similarity)
Subcellular location: Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side
Sequence caution: Sequence=BAD93116.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: Q59ED2 Q8N170
Alternative splicing: 2 isoforms:  O00469-1   O00469-2   

Explore the universe of human proteins at neXtProt for PLOD2: NX_O00469 

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


    • REFSEQ proteins (2 alternative transcripts): 
    NP_000926.2  NP_891988.1  


    ENSEMBL proteins: 
    ENSP00000419880 ENSP00000419963 ENSP00000420094 ENSP00000353170 ENSP00000282903 ENSP00000419354 


    Human Recombinant Proteins 
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Protein: PLOD2
    OriGene Protein Over-expression Lysate: PLOD2
    GenScript Custom Purified and Recombinant Proteins Services for PLOD2 
    Novus Biologicals Proteins for PLOD2
    Novus Biologicals Lysates for PLOD2
    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins

    3 Gene Ontology (GO) cellular component terms (GO ID links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005783 endoplasmic reticulum IEA--
    GO:0016020 membrane IEA--
    GO:0030867 rough endoplasmic reticulum membrane IEA--
    About this table

    PLOD2 for ontologies           About GeneDecksing



    Antibodies for PLOD2: 
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for PLOD2
    R&D Systems Antibodies for PLOD2 (Lysine Hydroxylase 2/PLOD2)
    Browse OriGene Antibodies
    GenScript Custom Superior Antibodies Services for PLOD2 
    Novus Biologicals Antibodies for PLOD2
    Browse antibodies at Epitomics

    Assays for PLOD2: 
    Browse Kits and Assays available from Millipore
    Browse ELISAs at Sigma-Aldrich
    OriGene Custom Immunoassay Development 
    Browse OriGene Fluorogenic Cell Assay Kits 
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for PLOD2 
    Browse Enzo Life Sciences for kits & assays
    Uscn ELISAs and CLIAs for PLOD2 

    Protein Domains/
    Families
    for PLOD2 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    PLOD2 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR006620 Pro_4_hyd_alph
     IPR001006 Procol_lys_dOase
     IPR005123 Oxoglutarate/Fe-dep_oxygenase

    Graphical View of Domain Structure for InterPro Entry O00469

    ProtoNet protein and cluster: O00469

    2 Blocks protein families:
    IPB001006 Procollagen-lysine 5-dioxygenase
    IPB006620 Prolyl 4-hydroxylase


    UniProtKB/Swiss-Prot: PLOD2_HUMAN, O00469
    Similarity: Contains 1 Fe2OG dioxygenase domain


    Gene Function
    for PLOD2 gene

    (According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
    About This Section

    UniProtKB/Swiss-Prot: PLOD2_HUMAN, O00469
    Function: Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of
    attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links
    Catalytic activity: L-lysine-[procollagen] + 2-oxoglutarate + O(2) = (2S,5R)-5-hydroxy-L-lysine-[procollagen] +
    succinate + CO(2)
    Enzyme Number (IUBMB): EC 1.14.11.4 

    Inhib.
    RNA:            		Browse for Gene Knock-down Tools from Millipore
    Browse Nano Scale siRNA at Sigma-Aldrich
    Sigma-Aldrich siRNA Panels and esiRNA and siRNA for PLOD2
    Sigma-Aldrich shRNA for PLOD2
    OriGene 29mer shRNA kits in GFP-retroviral vector (see all 2): PLOD2
    OriGene shRNA RFP (see all 2): PLOD2
    OriGene basic RS shRNA (see all 2): PLOD2
    OriGene siRNA (see all 2): PLOD2
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of PLOD2 
    miRNA:Sigma-Aldrich microRNA Mimics for PLOD2
    Browse microRNA target validation systems at Sigma-Aldrich 
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PLOD2 
    7 SABiosciences Assays for microRNAs that regulate PLOD2:
    hsa-miR-498 hsa-miR-1271 hsa-miR-26a hsa-miR-24 hsa-miR-96 hsa-miR-26b hsa-miR-1297

    Gene
    Editing:    		Browse CompoZr Knockout ZFN at Sigma-Aldrich 

    Clones:Browse Clones for the Expression of Recombinant Proteins Available from Millipore
    Browse iPSC Reprogramming Factors at Sigma-Aldrich
    OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): PLOD2
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): PLOD2
    OriGene untagged cDNA clones in CMV expression vector (see all 2): PLOD2
    OriGene 3'-UTR clone (see all 2): PLOD2 
    Browse MicroRNA Expression Plasmids 
    GenScript cDNA clones with any tag delivered in your preferred vector (see all 2): PLOD2 
    Browse Sino Biological Human cDNA Clones

    Cell
    Lines:          		GenScript Custom overexpressing Cell Line Services for PLOD2 

    Genatlas biochemistry entry for PLOD2:
    procollagen-lysine,2-oxoglutarate 5 dioxygenase 2

    5/9 Gene Ontology (GO) molecular function terms (GO ID links to tree view) (see all 9):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004866 endopeptidase inhibitor activity ----
    GO:0005506 iron ion binding IEA--
    GO:0005515 protein binding IPI17353931
    GO:0008475 procollagen-lysine 5-dioxygenase activity IEA--
    GO:0016491 oxidoreductase activity ----
    About this table

    PLOD2 for ontologies           About GeneDecksing


    Pathways & Interactions
    for PLOD2 gene

    (Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
    About This Section


    PLOD2 for pathways           About GeneDecksing

    1 Sigma-Aldrich "Your Favorite Gene" (powered by Ingenuity) Pathway for  PLOD2
        Lysine Degradation

    1 Kegg Pathway  (Kegg details for PLOD2):
        hsa00310 Lysine degradation

        SABiosciences Custom Pathway-Focused PCR Arrays for PLOD2 

        Sigma-Aldrich "Your Favorite Gene" (powered by Ingenuity) Molecular Interaction Network for PLOD2
        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PLOD2

    5/12 Interacting proteins for PLOD2 (O004691 ENSP000002829033) via UniProtKB, MINT, and/or STRING (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RUVBL2Q9Y2301EBI-1047459,EBI-352939
    NSD1ENSP000003480313STRING: ENSP00000348031
    DOT1LENSP000002214823STRING: ENSP00000221482
    EHMT1ENSP000002987283STRING: ENSP00000298728
    SETD1AENSP000002625193STRING: ENSP00000262519
    About this table

    3 Gene Ontology (GO) biological process terms (GO ID links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001666 response to hypoxia IEP15174142
    GO:0006464 protein modification process TAS9054364
    GO:0055114 oxidation-reduction process IEA--
    About this table

    PLOD2 for ontologies           About GeneDecksing



    Drugs & Compounds
    for PLOD2 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    PLOD2 for compounds           About GeneDecksing

    Browse Small Molecules at Sigma-Aldrich
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PLOD2
    3 Novoseek chemical compound relationships for PLOD2 gene
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hydroxylysinonorleucine 87.3 2 15589118 (1)
    pyridinoline 65 5 12881513 (3), 15296939 (1)
    lysine 57.7 5 10457259 (2), 15523625 (1), 15589118 (1), 12881513 (1)
    About this table



    Transcripts
    for PLOD2 gene

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Millipore,
    siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
    Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
    About This Section
    Inhib.
    RNA:             		Browse for Gene Knock-down Tools from Millipore
    Browse Nano Scale siRNA at Sigma-Aldrich
    Sigma-Aldrich siRNA Panels and esiRNA and siRNA for PLOD2
    Sigma-Aldrich shRNA for PLOD2
    OriGene 29mer shRNA kits in GFP-retroviral vector (see all 2): PLOD2
    OriGene shRNA RFP (see all 2): PLOD2
    OriGene basic RS shRNA (see all 2): PLOD2
    OriGene siRNA (see all 2): PLOD2
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of PLOD2 
    miRNA: Sigma-Aldrich microRNA Mimics for PLOD2
    Browse microRNA target validation systems at Sigma-Aldrich 
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PLOD2 
    7 SABiosciences Assays for microRNAs that regulate PLOD2:
    hsa-miR-498 hsa-miR-1271 hsa-miR-26a hsa-miR-24 hsa-miR-96 hsa-miR-26b hsa-miR-1297
    Clones: Browse FLAG tag genes at Sigma-Aldrich
    OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): PLOD2
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): PLOD2
    OriGene untagged cDNA clones in CMV expression vector (see all 2): PLOD2
    OriGene 3'-UTR Clone (see all 2): PLOD2 
    Browse OriGene MicroRNA Expression Plasmids 
    GenScript cDNA clones with any tag delivered in your preferred vector (see all 2): PLOD2 
    Primers: OriGene genome-wide validated SYBR primer pairs: PLOD2
    Browse OriGene validated miRNA SYBR primer pairs 
    SABiosciences RT2 qPCR Primer Assay for PLOD2: PPH09151A

    REFSEQ mRNAs for PLOD2 gene (2 alternative transcripts): 

    NM_000935.2  NM_182943.2  

    Additional cDNA sequence: 

    AB209879.1 AK125700.1 AK130098.1 AK295084.1 AL832238.1 BC016834.1 BC037169.1 U84573.1 

    8 DOTS entries:

    DT.455092  DT.92437003  DT.100646064  DT.100791553  DT.101983712  DT.92437010  DT.95374168  DT.120855559 

    24/230 AceView cDNA sequences (see all 230):

    AA306948 AW664579 AI678677 AI376301 AA370532 AV701704 N47487 BC016834 
    BQ007056 AL710984 BU660937 CA442925 AL705614 BC037169 AK130098 BQ227676 
    BF590307 BU678864 BG164395 CA445993 AI371427 CB135003 AA376884 BM724669 

    highest scoring ESTs for PLOD2:

    U84573 AI752235 AL705614 AV725327 BC037169 BG771978 BI457665 BI550032 BI551605 BI553359 

    Unigene Cluster for PLOD2:

    Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2
    Hs.477866  [show with all ESTs]
    Unigene Representative Sequence: NM_182943


    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for PLOD2

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
    SP1:                                                                    -                                                               
    SP2:                                                                    -                       -                                       
    SP3:                                                                                                                                    

    About this scheme

    ECgene alternative splicing isoforms for PLOD2
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000475505 ENST00000480704 ENST00000460520 ENST00000469350 ENST00000494950
    ENST00000360060 ENST00000495700 ENST00000282903(uc011bnm.1 uc003evr.1 uc003evs.1)
    ENST00000478436 ENST00000461497(uc003evq.1)

    Expression
    for PLOD2 gene

    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Primers from OriGene and/or SABiosciences )
    About This Section

    PLOD2 expression in normal and diseased human tissues

    1  / 2  / 3

    5 probe-sets matching PLOD2 gene

    Affymetrix
    probe-set    		 Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    34795_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 U84573 1.00 1.00 1.00 1
    202619_s_at2, 3 U133-A 1 1.00 1.00 -- -- AI754404 0.60 1.00 0.82 1
    202620_s_at2, 3 U133-A 1 1.00 1.00 -- -- NM_000935 0.60 1.00 0.82 1
    202619_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    202620_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table

    PLOD2 for expression           About GeneDecksing

    Data from Genenote  (Publications) and GNF BioGPS
        About these images
    PLOD2 gene expression
    PLOD2 gene electronic northern expression
    PLOD2 gene sage expression
    About these images

    CGAP SAGE TAG: TGTTAGAAAA

    SOURCE GeneReport for Unigene cluster: Hs.477866

    Expression variation in blood from EXPOLDB for PLOD2

    UniProtKB/Swiss-Prot: PLOD2_HUMAN, O00469
    Tissue specificity: Highly expressed in pancreas and muscle. Isoform 1 and isoform 2 are expressed in the majority of
    the examined cell types. Isoform 2 is specifically expressed in skin, lung, dura and aorta

    Primers: OriGene genome-wide validated SYBR primer pairs: PLOD2
    Browse OriGene validated miRNA SYBR primer pairs 
    SABiosciences RT2 qPCR Primer Assay for PLOD2: PPH09151A
        SABiosciences Custom PCR Arrays for PLOD2 


    Orthologs
    for PLOD2 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section
    Orthologs for PLOD2 gene from 5/10 species (see all 10)
    Organism Gene Locus Description Human
    Similarity    		 NCBI accessions
    dog
    (Canis familiaris)    		 PLOD21   -- procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 93.45(n)
    95.19(a)    		 485702  XM_542822.2  XP_542822.2 
    chimpanzee
    (Pan troglodytes)    		 PLOD21   -- procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 97.97(n)
    97.6(a)    		 460754  XM_516801.2  XP_516801.2 
    cow
    (Bos taurus)    		 PLOD21   -- procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 93.36(n)
    94.99(a)    		 533642  XM_613110.3  XP_613110.3 
    rat
    (Rattus norvegicus)    		 Plod21   -- procollagen lysine, 2-oxoglutarate 5-dioxygenase 2 86.5(n)
    90.37(a)    		 300901  NM_175869.2  NP_787065.1 
    mouse
    (Mus musculus)    		 Plod21 , 5 9 (48.40 cM)5
    		 procollagen lysine, 2-oxoglutarate 5-dioxygenase 21, 5 87.46(n)1
    90.83(a)1    		 264321  NM_011961.21  NP_036091.11 
     AA1255645  AA4742365  (see all 20)
    About this table        Species with no ortholog for PLOD2

    ENSEMBL Gene Tree for PLOD2 (if available)

    Paralogs
    for PLOD2 gene

    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section
    Paralogs for PLOD2 gene
    GLT25D12  GLT25D22  PLOD32  CERCAM2  PLOD12  

    PLOD2 for paralogs           About GeneDecksing



    Genomic Variants
    for PLOD2 gene

    (SNPs according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
    About This Section

    10/862 NCBI SNPs in PLOD2 are shown (see all 862)
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidChr 3 posSequenceRecsAA
    Chg    		TypeMoreRecsAllele
    freq    		PopTotal
    sample    		More
    ----------
    rs67101,2
    		C,F,A,145788467(-) TTTGGG/ATGAAT 1 -- ut3116Minor allele frequency- A:0.49MN NS EA NA WA 1038
    rs7647551,2
    		C,F,O,A,145801118(+) AGAAGC/GTAGAA 2 -- int126Minor allele frequency- G:0.47EA NA NS WA 1140
    rs8959281,2
    		C,F,H,145844239(+) GAAAAT/CGTAAC 2 -- int111Minor allele frequency- C:0.01NS EA NA WA 432
    rs8959291,2
    		C,F,A,145844410(+) agacaC/Gaaaag 2 -- int1 trp313Minor allele frequency- G:0.50NS EA NA WA 642
    rs8959301,2
    		C,F,A,H,145844473(+) gtcacA/Ggacct 2 -- int113Minor allele frequency- G:0.50NS EA NA WA 642
    rs9593291,2
    		C,F,O,A,145801162(+) TCTACC/TCTTCA 2 -- int120Minor allele frequency- A:0.11NS EA NA WA 964
    rs9635911,2
    		C,F,A,H,145793825(-) tggtgA/Ttggga 2 -- int110Minor allele frequency- T:0.49NA EA WA 224
    rs9650311,2
    		H145864413(+) TGGGCA/GTAAGG 2 -- int14Minor allele frequency- G:0.00NS EA 420
    rs9650321,2
    		C,F,A,145864511(+) TCCCCA/GCTGGG 2 -- int119Minor allele frequency- G:0.23NA EA NS WA 616
    rs10612601,2
    		--145787301(-) AAATTC/TTTAAT 1 -- ut311Minor allele frequency- T:0.00MN 184
    About this table

    HapMap Linkage Disequilibrium images for PLOD2 (up to first 250kb)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for PLOD2: --

    QIAGEN SeqTarget long-range PCR primers for resequencing PLOD2 

    Disorders & Mutations
    for PLOD2 gene

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    PLOD2 for disorders           About GeneDecksing

    OMIM: 601865   disorders: 609220  

    UniProtKB/Swiss-Prot: PLOD2_HUMAN, O00469

  • Defects in PLOD2 are the cause of Bruck syndrome type 2 (BRKS2) [MIM:609220]. Bruck syndrome, also known as
    • osteogenesis imperfecta with congenital joint contractures, is an autosomal recessive disease characterized by
    generalized osteopenia, joint contractures at birth, fragile bones and short stature. It can be distinguished from
    osteogenesis imperfecta by the absence of hearing loss and dentinogenesis imperfecta, and by the presence of clubfoot
    and congenital joint limitations. The molecular defect is an aberrant cross-linking of bone collagen, due to
    underhydroxylation of lysine residues within the telopeptides of type I collagen, whereas the lysine residues in the
    triple helix are normal

    4 Novoseek disease relationships for PLOD2 gene

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    eds vi 84 1 15589118 (1)
    connective tissue diseases 57.9 1 15694128 (1)
    sclerosis systemic 45.5 2 16139999 (1), 12881513 (1)
    contracture 42.1 1 15523624 (1)
    About this table

    Locus Specific Mutation Databases (LSDB): PLOD2
    Human Gene Mutation Database (HGMD): PLOD2
    Human Genome Epidemiology (HuGE) Navigator: PLOD2 (3 documents)

    Export disorders and mutations for PLOD2 gene to outside databases

    Medical News
    for PLOD2 gene

    (Possibly Related Articles in Doctor's Guide)
    About This Section
    		   --

    Publications
    for PLOD2 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6UniProtKB/TrEMBL, and/or 7Novoseek)
    About This Section

    10/45 PubMed articles for PLOD2 gene, integrated from 7 sources (see all 45):
    (articles sorted by number of sources associating them with PLOD2)
    1. Cloning and characterization of a novel human lysyl hydroxylase isoform highly expressed in pancreas and muscle. (PubMed id 9054364)1, 2, 3, 7 Valtavaara M....Myllylae R. (1997)
    2. Identification of PLOD2 as telopeptide lysyl hydroxylase, an important enzyme in fibrosis. (PubMed id 12881513)1, 2, 7 van der Slot A.J.... Bank R.A. (2003)
    3. Phenotypic and molecular characterization of Bruck syndrome (osteogenesis imperfecta with contractures of the large joints) caused by a recessive mutation in PLOD2. (PubMed id 15523624)1, 2, 7 Ha-Vinh R.... Bonafe L. (2004)
    4. Tissue specificity of a new splice form of the human lysyl hydroxylase 2 gene. (PubMed id 10372558)1, 2, 7 Yeowell H.N. and Walker L.C. (1999)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    6. Tissue-specific expression and regulation of the alternatively-spliced forms of lysyl hydroxylase 2 (LH2) in human kidney cells and skin fibroblasts. (PubMed id 15694128)1, 7 Walker L.C....Yeowell H.N. (2005)
    7. Decreased expression of lysyl hydroxylase 2 (LH2) in skin fibroblasts from three Ehlers-Danlos patients does not result from mutations in either the coding or proximal promoter region of the LH2 gene. (PubMed id 15589118)1, 7 Walker L.C....Yeowell H.N. (2004)
    8. Fox-2 protein regulates the alternative splicing of s cleroderma-associated lysyl hydroxylase 2 messenger RNA. (PubMed id 20131247)1, 7 Seth P. and Yeowell H.N. (2010)
    9. Lack of collagen type specificity for lysyl hydroxylase isoforms. (PubMed id 10701773)1, 7 Wang C....Myllyla R. (2000)
    10. Functional diversity of lysyl hydroxylase 2 in collagen synthesis of human dermal fibroblasts. (PubMed id 16934803)1, 7 Wu J....Brinckmann J. (2006)

    External Searches for PLOD2 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
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      Query String
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    Genome Databases showing PLOD2 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 5352 HGNC: 9082 AceView: PLOD2 Ensembl:ENSG00000152952 euGenes: HUgn5352
    ECgene: PLOD2 Kegg: 5352 H-InvDB: PLOD2

    Other Databases showing PLOD2 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing PLOD2 gene

    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    Osteogenesis imperfecta variant databasehttp://oi.gene.le.ac.uk/home.php?select_db=PLOD2

    Intellectual Property
    for PLOD2 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from XenneX, Inc.)
    About This Section
    		Patent Information for PLOD2 gene:
    Search GeneIP for patents involving PLOD2

    GeneCards and IP:
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    Products
    for PLOD2 gene

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    Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or Enzo Life Sciences)
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