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PDCD2L Gene

protein-coding   GIFtS: 47
GCID: GC19P034895

Programmed Cell Death 2-Like

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Programmed Cell Death 2-Like1 2
Programmed Cell Death Protein 2-Like2
MGC130965

External Ids:    HGNC: 281941   Entrez Gene: 843062   Ensembl: ENSG000001262497   OMIM: 6156615   UniProtKB: Q9BRP13   
ORGUL members:         

Export aliases for PDCD2L gene to outside databases

Previous GC identifers: GC19P039588 GC19P031401


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for PDCD2L Gene:
PDCD2L (programmed cell death 2-like) is a protein-coding gene. Diseases associated with PDCD2L include malaria. An important paralog of this gene is ENSG00000266953.

UniProtKB/Swiss-Prot: PDD2L_HUMAN, Q9BRP1
Function: Over-expression suppresses AP1, CREB, NFAT, and NF-kB transcriptional activation, and delays cell cycle
progression at S phase




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000019.10  NC_018930.2  NT_011109.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the PDCD2L gene promoter:
         RFX1   AML1a   AP-4   HNF-4alpha1   E47   Arnt   Egr-4   Egr-2   HOXA5   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPDCD2L promoter sequence
   Search Chromatin IP Primers for PDCD2L

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PDCD2L


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

Entrez Gene cytogenetic band: 19q13.11   Ensembl cytogenetic band:  19q13.11   HGNC cytogenetic band: 19q13.11

PDCD2L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PDCD2L gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P034895:  view genomic region     (about GC identifiers)

Start:
34,895,289 bp from pter      End:
34,917,073 bp from pter
Size:
21,785 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: PDD2L_HUMAN, Q9BRP1 (See protein sequence)
Recommended Name: Programmed cell death protein 2-like  
Size: 358 amino acids; 39417 Da

Explore the universe of human proteins at neXtProt for PDCD2L: NX_Q9BRP1

Explore proteomics data for PDCD2L at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys6
  • Modification sites at PhosphoSitePlus

  • See PDCD2L Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_115722.1  
    ENSEMBL proteins: 
     ENSP00000246535   ENSP00000475984  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR007320 PDCD2_C

    Graphical View of Domain Structure for InterPro Entry Q9BRP1

    ProtoNet protein and cluster: Q9BRP1

    1 Blocks protein domain: IPB007320 Programmed cell death protein 2


    PDCD2L for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PDD2L_HUMAN, Q9BRP1
    Function: Over-expression suppresses AP1, CREB, NFAT, and NF-kB transcriptional activation, and delays cell cycle
    progression at S phase

    Animal Models:

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PDCD2L
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular2
    cytosol1
    mitochondrion1
    nucleus1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--

    PDCD2L for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PDCD2L
    Interactions:

        Search GeneGlobe Interaction Network for PDCD2L

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    Selected Interacting proteins for PDCD2L (Q9BRP13 ENSP000002465354) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SLX4Q8IY923, ENSP000002940084I2D: score=1 STRING: ENSP00000294008
    CAMKK2Q96RR43I2D: score=1 
    WIPI2Q9Y4P83I2D: score=1 
    PSMD2ENSP000003101294STRING: ENSP00000310129
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007049cell cycle IEA--

    PDCD2L for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PDCD2L (PDD2L)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PDCD2L gene: 
    NM_032346.1  

    Unigene Cluster for PDCD2L:

    Programmed cell death 2-like
    Hs.515344  [show with all ESTs]
    Unigene Representative Sequence: BU163947
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000246535(uc002nvj.3) ENST00000587385 ENST00000587065 ENST00000585821
    ENST00000589589
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat PDCD2L
      QuantiFast Probe-based Assays in human, mouse, rat PDCD2L

    Additional mRNA sequence: BC006146.1 

    11 DOTS entries:

    DT.412770  DT.100716842  DT.97842044  DT.100729227  DT.99958138  DT.92422946  DT.121476563  DT.95270961 
    DT.100674903  DT.100864718  DT.101968887 

    Selected AceView cDNA sequences (see all 1209):

    BM014161 BM928698 BQ049018 AW962044 BQ691326 AI191757 BE263710 BQ573898 
    BU739343 BQ688472 BU174967 BQ225446 BM904384 F29189 BF062457 BM469077 
    AU124847 BM790934 BP362614 AU121930 BP335759 BP364949 BQ896923 BU674480 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for PDCD2L    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7
    SP1:                                -                                 
    SP2:                    -           -                                 
    SP3:                                -                                 
    SP4:                                                                  


    ECgene alternative splicing isoforms for PDCD2L

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PDCD2L expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAAGAATTTT
    PDCD2L Expression
    About this image

    PDCD2L Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PDCD2L Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.515344

    UniProtKB/Swiss-Prot: PDD2L_HUMAN, Q9BRP1
    Tissue specificity: Higher expression in lung, colon, mammary gland, cervix, stomach and small intestine

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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for PDCD2L gene from Selected species (see all 18)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pdcd2l1 , 5 programmed cell death 2-like1, 5 79.31(n)1
    72.19(a)1
      7 (19.45 cM)5
    680791  NM_026549.31  NP_080825.11 
     341844995 
    chicken
    (Gallus gallus)
    Aves PDCD2L1 programmed cell death 2-like 63.76(n)
    53.65(a)
      415785  NM_001030572.1  NP_001025743.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    44(a)
    1 → many
    GL344074.1(22981-30784)
    African clawed frog
    (Xenopus laevis)
    Amphibia BU899451.12   -- 77.86(n)    BU899451.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC046049.12   -- 74.5(n)   393192  BC046049.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta trus1 toys are us 48.4(n)
    39.22(a)
      41540  NM_141948.2  NP_650205.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G648301 AT5G64830 45.29(n)
    32.89(a)
      836606  NM_125881.3  NP_201288.1 
    rice
    (Oryza sativa)
    Liliopsida Os04g06408001 Os04g0640800 43.88(n)
    30.61(a)
      4337167  NM_001060574.1  NP_001054039.1 


    ENSEMBL Gene Tree for PDCD2L (if available)
    TreeFam Gene Tree for PDCD2L (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PDCD2L gene
    ENSG000002669532  PDCD22  

    PDCD2L for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for PDCD2L
    PGOHUM00000242194


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PDCD2L (see all 441)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1439024211,2
    --34893897(+) ATCCCA/GACTCC 1 -- us2k10--------
    rs1843472881,2
    --34894497(+) GTGGTC/GGTGGG 1 -- us2k10--------
    rs784132701,2
    C,F--34894595(+) CACTTC/AAGCCT 1 -- us2k11Minor allele frequency- A:0.03NA 120
    rs1902853591,2
    --34894669(+) AATCTC/GAAACA 1 -- us2k10--------
    rs15591951,2
    C,F,O,A,H--34894820(-) ACACAC/TCAAAA 1 -- us2k125Minor allele frequency- T:0.15MN NS EA NA WA CSA 2586
    rs799219711,2
    C,F--34894939(+) TTCTGG/ATGGCT 1 -- us2k11Minor allele frequency- A:0.02EA 120
    rs58279011,2
    C,F--34894997(+) TTGAA-/CCCCAG 1 -- us2k15Minor allele frequency- C:0.40NA CSA 10
    rs1824606651,2
    --34895072(+) GTTAGC/TTTTTT 1 -- us2k10--------
    rs589121521,2
    C,F--34895166(+) CGAGCC/TCCTGA 1 -- us2k12Minor allele frequency- T:0.08WA 120
    rs1142409531,2
    --34895204(+) ACCTGA/CGCGCA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for PDCD2L (34895289 - 34917073 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for PDCD2L:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509738CNV Insertion20534489

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PDCD2L
    DNA2.0 Custom Variant and Variant Library Synthesis for PDCD2L

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 615661    OMIM disorders: --

    1 disease for PDCD2L:    
    About MalaCards
    malaria


    PDCD2L for disorders           About GeneDecksing


    Export disorders for PDCD2L gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PDCD2L gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with PDCD2L)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The novel MGC13096 protein is correlated with proliferation. (PubMed id 17393540)1, 2 Chen Q.... Qian K. (Cell Biochem. Funct. 2008)
    2. Cloning of cDNAs with PDCD2(C) domain and their expressions during apoptosis of HEK293T cells. (PubMed id 16311922)1, 3 Chen Q....Yan C. (Mol. Cell. Biochem. 2005)
    3. 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. (Genome Res. 2004)
    4. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    5. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    6. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    8. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    9. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    10. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 84306 HGNC: 28194 AceView: GPIandMGC13096 Ensembl:ENSG00000126249 euGenes: HUgn84306
    ECgene: PDCD2L H-InvDB: PDCD2L

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for PDCD2L Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PDCD2L gene:
    Search GeneIP for patents involving PDCD2L

    GeneCards and IP:
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