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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CDR2 Gene

protein-coding   GIFtS: 55
GCID: GC16M022357

Cerebellar Degeneration-Related Protein 2, 62kDa

(Previous name: cerebellar degeneration-related protein (62kD))
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Cerebellar Degeneration-Related Protein 2, 62kDa1 2     CDR622
Yo Paraneoplastic Antigen1 2     Yo2
Major Yo Paraneoplastic Antigen2 3     Cerebellar Degeneration-Related Protein 22
Paraneoplastic Cerebellar Degeneration-Associated Antigen2 3     PCD173
Cerebellar Degeneration-Related Protein (62kD)1     

External Ids:    HGNC: 17991   Entrez Gene: 10392   Ensembl: ENSG000001407437   OMIM: 1173405   UniProtKB: Q018503   

Export aliases for CDR2 gene to outside databases

Previous GC identifers: GC16M021758 GC16M022365 GC16M022323 GC16M022264 GC16M020602


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for CDR2 Gene: 
CDR2 (cerebellar degeneration-related protein 2, 62kDa) is a protein-coding gene. Diseases associated with CDR2 include gait apraxia, and paraneoplastic cerebellar degeneration. GO annotations related to this gene include protein binding and molecular_function. An important paralog of this gene is CDR2L.

Gene Wiki entry for CDR2 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NC_018927.2  NT_010393.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CDR2 gene promoter:
         HOXA9   AhR   ISGF-3   LHX3b/Lhx3b   XBP-1   POU3F2   RORalpha2   LHX3a/Lhx3a   Meis-1a   TGIF   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCDR2 promoter sequence
   Search SABiosciences Chromatin IP Primers for CDR2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CDR2


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

Entrez Gene cytogenetic band: 16p12.3   Ensembl cytogenetic band:  16p12.2   HGNC cytogenetic band: 16p13.1-p12

CDR2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CDR2 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M022357:  view genomic region     (about GC identifiers)

Start:
22,357,257 bp from pter      End:
22,448,486 bp from pter
Size:
91,230 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CDR2_HUMAN, Q01850 (See protein sequence)
Recommended Name: Cerebellar degeneration-related protein 2  
Size: 454 amino acids; 51855 Da
Sequence caution: Sequence=AAA51961.1; Type=Frameshift; Positions=379, 384, 393; Sequence=AAB20813.1;
Type=Erroneous initiation; Sequence=BAA02360.1; Type=Erroneous initiation;
Secondary accessions: A8K8A8 Q13977

Explore the universe of human proteins at neXtProt for CDR2: NX_Q01850

Explore proteomics data for CDR2 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q01850

  • CDR2 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CDR2 Protein Expression
    REFSEQ proteins: NP_001793.1  
    ENSEMBL proteins: 
     ENSP00000268383   ENSP00000457432   ENSP00000455915   ENSP00000457289   ENSP00000457596  
     ENSP00000454706  

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    Cloud-Clone Corp. Proteins for CDR2 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus NAS--
    GO:0005737cytoplasm IEA--

    CDR2 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR026079 CDR2

    Graphical View of Domain Structure for InterPro Entry Q01850

    ProtoNet protein and cluster: Q01850

    UniProtKB/Swiss-Prot: CDR2_HUMAN, Q01850
    Similarity: Belongs to the CDR2 family


    CDR2 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:
         Genatlas biochemistry entry for CDR2:
    cerebellar degeneration-related major antigen,62kDa,putative neuronal signal transduction protein,identified using
    antisera Yo from patients with breast and ovarian cancers and a paraneoplastic neurologic disorder

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005515protein binding IPI11988016
         
    CDR2 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for CDR2:
     Decreased viability of wild-ty 

         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Cdr2):
     normal 

    CDR2 for phenotypes           About GeneDecksing

    Animal Models:
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CDR2 
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for CDR2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    5/11 Interacting proteins for CDR2 (Q018501, 3 ENSP000002683834) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MORF4L2Q150141, 3EBI-1181367,EBI-399257 I2D: score=3 
    ASS1P009663, ENSP000002530044I2D: score=2 STRING: ENSP00000253004
    MYCP011063, ENSP000003672074I2D: score=2 STRING: ENSP00000367207
    FOLR2P142073, ENSP000002982234I2D: score=1 STRING: ENSP00000298223
    PKN1Q165123, ENSP000003433254I2D: score=3 STRING: ENSP00000343325
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CDR2

    Search CenterWatch for drugs/clinical trials and news about CDR2

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CDR2 gene: 
    NM_001802.1  

    Unigene Cluster for CDR2:

    Cerebellar degeneration-related protein 2, 62kDa
    Hs.513430  [show with all ESTs]
    Unigene Representative Sequence: BC017503
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000268383(uc002dkn.3) ENST00000564542 ENST00000561630 ENST00000567406
    ENST00000567010 ENST00000563573 ENST00000569045
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    Additional mRNA sequence: 

    AK292273.1 BC017503.1 D12981.1 M63256.1 

    7 DOTS entries:

    DT.97842518  DT.75103832  DT.416005  DT.91803187  DT.120658652  DT.92453494  DT.92453499 

    24/278 AceView cDNA sequences (see all 278):

    AL041649 BQ637118 BC050479 BF003026 AA043995 BQ014651 AA235665 AA074613 
    CR617156 AI369418 AW850627 BQ019251 AI096381 N54583 AL041501 BM857639 
    BI869500 AL041502 BF001768 AA831448 AL041650 BU685879 BM682267 BE222026 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for CDR2    About this scheme

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


    ECgene alternative splicing isoforms for CDR2

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CDR2 expression in normal human tissues (normalized intensities)      CDR2 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACAAACTGGC
    CDR2 Expression
    About this image


    CDR2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/1 selected tissues (see all 1) fully expand
     
     Brain (Nervous System)    fully expand to see all 16 entries
             Globus Pallidus
             Septum   

     -- (Endocrine System)
             Pituitary gland   

    See CDR2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CDR2

    SOURCE GeneReport for Unigene cluster: Hs.513430
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    In Situ
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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for CDR2 gene from 6/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cdr21 , 5 cerebellar degeneration-related 21, 5 85.87(n)1
    89.18(a)1
      7 (65.04 cM)5
    125851  NM_007672.21  NP_031698.21 
     1209570365 
    chicken
    (Gallus gallus)
    Aves CDR21 cerebellar degeneration-related protein 2, 62kDa 69.78(n)
    72.38(a)
      416621  NM_001030642.1  NP_001025813.1 
    lizard
    (Anolis carolinensis)
    Reptilia CDR26
    Uncharacterized protein
    69(a)
    1 ↔ 1
    GL343846.1(11243-21061)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.47452 Transcribed sequence with weak similarity to protein pirA40448 (H.sapiens) A40448 DNA-binding protein CDR-62 - human (fragment) less 76.26(n)    BQ388488.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1001481751 cerebellar degeneration-related protein 2-like 57.47(n)
    51.32(a)
      100148175  XM_001921397.2  XP_001921432.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta Cen6
    Centrocortin
    11(a)
    1 → many
    2L(20678921-20681844)


    ENSEMBL Gene Tree for CDR2 (if available)
    TreeFam Gene Tree for CDR2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CDR2 gene
    CDR2L2  
    1 SIMAP similar gene for CDR2 using alignment to 6 protein entries:     CDR2_HUMAN (see all proteins):
    CDR2L

    CDR2 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for CDR2
    PGOHUM00000235530


    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/520 SNPs in CDR2 are shown (see all 520)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2007674581,2
    C--22356893(+) ACATT-/AATAGT
    ATAGTTTG
    AATAG
    1 -- ds50010--------
    rs1401167791,2
    --22356929(+) AGTATA/GGTTTC 1 -- ds50010--------
    rs2015568111,2
    --22357016(+) GAAAT-/AGTG  
            
    AAAAT
    1 -- ds50010--------
    rs1421240021,2
    C--22357231(+) TTATAC/TTGAAA 1 -- ds50010--------
    rs1834821281,2
    --22357234(+) TATTGA/GAAGTA 1 -- ds50010--------
    rs1880885381,2
    --22357310(+) TAATCA/GGAACA 1 -- ut310--------
    rs567729321,2
    C--22357373(+) CAGTC-/AGAAGATC 1 -- cds11Minor allele frequency- AGA:0.50CSA 2
    rs2019306631,2
    C--22357378(-) GTATTC/GATCTG 1 -- ut310--------
    rs1463753231,2
    --22357438(+) GGAATC/GGTAAG 1 -- ut310--------
    rs1927048381,2
    --22357542(+) TTGAGA/GAAGTG 1 -- ut310--------

    HapMap Linkage Disequilibrium report for CDR2 (22357257 - 22448486 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/15 variations for CDR2 (see all 15):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2714070CNV Deletion23290073
    nsv435668CNV Deletion17901297
    dgv48n16CNV Insertion17901297
    nsv1764CNV Loss18451855
    nsv498860CNV Loss21111241
    dgv2647n71CNV Loss21882294
    nsv9404CNV Gain18304495
    nsv519813CNV Gain+Loss19592680
    dgv834e1CNV Complex17122850
    nsv7280OTHER Inversion18451855

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 117340    OMIM disorders: --

    12 diseases for CDR2:    About MalaCards
    gait apraxia    paraneoplastic cerebellar degeneration    cerebellar degeneration    paraneoplastic neurologic disorders
    papillary renal cell carcinoma    apraxia    candidiasis    severe combined immunodeficiency
    renal cell carcinoma    ovarian cancer    neuronitis    breast cancer

    1 disease from the University of Copenhagen DISEASES database for CDR2:
    Gait apraxia

    CDR2 for disorders           About GeneDecksing

    5 Novoseek inferred disease relationships for CDR2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    paraneoplastic cerebellar degeneration 97 10 18053582 (2), 10465786 (1), 10500270 (1), 8545049 (1) (see all 9)
    cerebellar degeneration 86.6 5 10465786 (1), 16542365 (1), 19581925 (1), 18053582 (1)
    ovarian cancer 20.1 2 10786675 (1)
    tumors 11.4 23 19581925 (4), 10786675 (3), 10465786 (2), 20383333 (2) (see all 5)
    cancer 8.71 2 10786675 (1)

    Genetic Association Database (GAD): CDR2
    Human Genome Epidemiology (HuGE) Navigator: CDR2 (1 document)

    Export disorders for CDR2 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 CDR2 gene, integrated from 9 sources (see all 43):
    (articles sorted by number of sources associating them with CDR2)
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    1. Cloning of a leucine-zipper protein recognized by the sera of patients with antibody-associated paraneoplastic cerebellar degeneration. (PubMed id 2014264)1, 2, 3 Fathallah-Shaykh H.... Furneaux H.M. (1991)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
    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. (2004)
    4. Isolation of a complementary DNA clone encoding an autoantigen recognized by an anti-neuronal cell antibody from a patient with paraneoplastic cerebellar degeneration. (PubMed id 1763903)1, 2 Sakai K....Steinman L. (1991)
    5. Isolation of a complementary DNA clone encoding an autoantigen recognized by an anti-neuronal cell antibody from a patient with paraneoplastic cerebellar degeneration. (PubMed id 2260856)1, 2 Sakai K.... Steinman L. (1990)
    6. Onconeuronal cerebellar degeneration-related antigen, Cdr2, is strongly expressed in papillary renal cell carcinoma and leads to att enuated hypoxic response. (PubMed id 19581925)1, 9 Balamurugan K....Camenisch G. (2009)
    7. The cytoplasmic Purkinje onconeural antigen cdr2 down-regulates c-Myc function: implications for neuronal and tumor cell survival. (PubMed id 10465786)1, 9 Okano H.J....Darnell R.B. (1999)
    8. PKN interacts with a paraneoplastic cerebellar degeneration-associated antigen, which is a potential transcription factor. (PubMed id 9637778)1, 9 Takanaga H....Ono Y. (1998)
    9. The onconeural antigen cdr2 is a novel APC/C target t hat acts in mitosis to regulate c-myc target genes in mammalian tumor cells. (PubMed id 20383333)1, 9 O'Donovan K.J....Darnell R.B. (2010)
    10. Onconeuronal antigen Cdr2 correlates with HIF prolyl-4 -hydroxylase PHD1 and worse prognosis in renal cell carcinoma. (PubMed id 23531419)1 Kaufmann M.R....Camenisch G. (2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1039 HGNC: 1799 AceView: CDR2 Ensembl:ENSG00000140743 euGenes: HUgn1039
    ECgene: CDR2 H-InvDB: CDR2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CDR2 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 CDR2 gene:
    Search GeneIP for patents involving CDR2

    GeneCards and IP:
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