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

CCRN4L Gene

protein-coding   GIFtS: 50
GCID: GC04P139936

CCR4 carbon catabolite repression 4-like (S. cerevisiae)

(Previous names: CCR4-like (carbon catabolite repression 4, S.cerevisiae)...)
 Explore 2 diseases affiliated with
CCRN4L via our new
 Human Malady Compendium 
Biological research products
for CCRN4L
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
CCR4 Carbon Catabolite Repression 4-Like (S. Cerevisiae)1 2     NOC2 3
CCR4L1 2 5     CCR4 Protein Homolog2 3
CCR41 3 5     Nocturnin1
CCR4-Like (Carbon Catabolite Repression 4, S.Cerevisiae)1 2     

External Ids:    HGNC: 142541   Entrez Gene: 258192   Ensembl: ENSG000001510147   OMIM: 6084685   UniProtKB: Q9UK393   

Export aliases for CCRN4L gene to outside databases

Previous GC identifers: GC04P140842 GC04P140236 GC04P140403 GC04P140514 GC04P140294 GC04P140156 GC04P135667


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

Entrez Gene summary for CCRN4L:
The protein encoded by this gene is highly similar to Nocturnin, a gene identified as a circadian clock regulated gene
in Xenopus laevis. This protein and Nocturnin protein share similarity with the C-terminal domain of a yeast
transcription factor, carbon catabolite repression 4 (CCR4). The mRNA abundance of a similar gene in mouse has been
shown to exhibit circadian rhythmicity, which suggests a role for this protein in clock function or as a circadian
clock effector. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: NOCT_HUMAN, Q9UK39
Function: Component of the circadian clock or downstream effector of clock function. Exhibits a high amplitude
circadian rhythm with maximal levels in early evening. In constant darkness or constant light, the amplitude of the
rhythm decreases (By similarity)

summary for CCRN4L:
Chemokines (chemotactic cytokines) belong to a family of chemoattractant molecules involved in the directed
migration of immune cells. Over fifty human chemokines have been identified that can be categorised into
four groups; CC, CXC, CX3C and C (XCL1 and XCL2); depending on the spacing of their first two cysteine
residues. Chemokines exert their effects by binding to G-protein-coupled chemokine receptors on the surface
of cells, predominantly leukocytes. Eighteen human chemokine receptors have been identified that are
classified according to the class of chemokines that they bind. The major function of chemokines is to
regulate leukocyte trafficking in hematopoiesis and in innate and adaptive immunity. Other functions include
angiogenic activity, apoptosis, T-cell differentiation and phagocyte activation. Inadvertent activation of
chemokine receptors leads to autoimmunity by inappropriately targeting self antigens for destruction by
cytotoxic T-cells and macrophages.




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.1  NT_016354.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CCRN4L gene promoter:
         Max1   AP-2gamma   NF-kappaB   Arnt   Roaz   AP-2beta   NF-kappaB1   AP-2alpha   AP-2alphaA   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CCRN4L promoter sequence
   Search SABiosciences Chromatin IP Primers for CCRN4L

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CCRN4L


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

Entrez Gene cytogenetic band: 4q31.1   Ensembl cytogenetic band:  4q31.1   HGNC cytogenetic band: 4q31.1

CCRN4L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCRN4L gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P139936:  view genomic region     (about GC identifiers)

Start:
139,936,943 bp from pter      End:
139,967,093 bp from pter
Size:
30,151 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: NOCT_HUMAN, Q9UK39 (See protein sequence)
Recommended Name: Nocturnin  
Size: 431 amino acids; 48196 Da
Secondary accessions: D3DNY5 Q14D51 Q9HD93 Q9HD94 Q9HD95

Explore the universe of human proteins at neXtProt for CCRN4L: NX_Q9UK39

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UK39

  • CCRN4L Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_036250.2  
    ENSEMBL proteins: 
     ENSP00000280614  
    Reactome Protein details: Q9UK39
    Human Recombinant Protein Products: 
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    Uscn Proteins for CCRN4L

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000932cytoplasmic mRNA processing body IEA--
    GO:0005634nucleus TAS10521507
    GO:0005654nucleoplasm TAS--


    CCRN4L for ontologies           About GeneDecksing



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

    CCRN4L for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR005135 Endo/exonuclease/phosphatase

    Graphical View of Domain Structure for InterPro Entry Q9UK39

    ProtoNet protein and cluster: Q9UK39

    UniProtKB/Swiss-Prot: NOCT_HUMAN, Q9UK39
    Similarity: Belongs to the CCR4/nocturin family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: NOCT_HUMAN, Q9UK39
    Function: Component of the circadian clock or downstream effector of clock function. Exhibits a high amplitude
    circadian rhythm with maximal levels in early evening. In constant darkness or constant light, the amplitude of the
    rhythm decreases (By similarity)

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CCRN4L
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    hsa-miR-1287 hsa-miR-875-3p hsa-miR-301a hsa-miR-499-5p hsa-miR-208b hsa-miR-208a hsa-miR-130b hsa-miR-301b
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCRN4L

    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003700sequence-specific DNA binding transcription factor activity TAS10521507


    CCRN4L for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Ccrn4ltm1Bjc for CCRN4L
         3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Ccrn4l):
     growth/size  homeostasis/metabolism  liver/biliary system 

    CCRN4L for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Circadian rhythm - mammal
    Circadian Clock0.41
    BMAL1:CLOCK/NPAS2 Activates Circadian Expression0.23
    2Expression of NOCTURNIN
    Expression of NOCTURNIN1.00
    3Cyclins and Cell Cycle Regulation
    Cell Cycle Control by BTG Proteins0.36

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for CCRN4L
        Cell Cycle Control by BTG Proteins

    3        Reactome Pathways for CCRN4L
        Circadian Clock
    BMAL1:CLOCK/NPAS2 Activates Circadian Expression
    Expression of NOCTURNIN



    CCRN4L for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CCRN4L

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for CCRN4L (ENSP000002806144) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARNTLENSP000003743574STRING: ENSP00000374357
    CLOCKENSP000003087414STRING: ENSP00000308741
    NPAS2ENSP000003382834STRING: ENSP00000338283
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000290deadenylation-dependent decapping of nuclear-transcribed mRNA IEA--
    GO:0006355regulation of transcription, DNA-dependent TAS10521507
    GO:0006366transcription from RNA polymerase II promoter TAS10521507
    GO:0033962cytoplasmic mRNA processing body assembly IEA--
    GO:0048511rhythmic process IEA--


    CCRN4L for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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

    Compounds for CCRN4L available from Tocris Bioscience    About this table
    CompoundAction CAS #
    C 021 dihydrochloridePotent CCR4 antagonist[864289-85-0]
    Search CenterWatch for drugs/clinical trials and news about CCRN4L / NOCT 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CCRN4L gene: 
    NM_012118.2  

    Unigene Clusters for CCRN4L:

    CCR4 carbon catabolite repression 4-like (S. cerevisiae)
    Hs.639842 , Hs.656047  [show with all ESTs]
    Unigene Representative Sequences: AF199494, NM_012118
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000280614(uc003ihk.1 uc003ihl.3) ENST00000515616

    miRNA
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    hsa-miR-1287 hsa-miR-875-3p hsa-miR-301a hsa-miR-499-5p hsa-miR-208b hsa-miR-208a hsa-miR-130b hsa-miR-301b
    SwitchGear 3'UTR luciferase reporter plasmidCCRN4L 3' UTR sequence
    Inhib. RNA
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    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CCRN4L
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CCRN4L
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CCRN4L

    Additional cDNA sequence: 

    AF183961.1 AF199493.1 BC021963.2 BC023512.2 BC077723.1 BC113494.1 BC113500.1 

    4 DOTS entries:

    DT.92021033  DT.40294720  DT.121274165  DT.95202697 

    1 AceView cDNA sequence:

    BV188040 

    GeneLoc Exon Structure


    (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

    CCRN4L expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CCCTTGGAAA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See CCRN4L Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CCRN4L

    SOURCE GeneReport for Unigene clusters: Hs.639842 Hs.656047
        SABiosciences Expression via Pathway-Focused PCR Array including CCRN4L: 
              Circadian Rhythms in human mouse rat

    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCRN4L

    (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 eukaryotes.

    Orthologs for CCRN4L gene from 7/22 species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves CCRN4L1 CCR4 carbon catabolite repression 4-like (S. cerevisiae) 76.49(n)
    82.57(a)
      404779  NM_001009928.1  NP_001009928.1 
    lizard
    (Anolis carolinensis)
    Reptilia CCRN4L6
    --
    75(a)
    1 ↔ 1
    5(120425364-120427077)
    African clawed frog
    (Xenopus laevis)
    Amphibia ccrn4l-A2 CCR4 carbon catabolite repression 4-like, nocturnin 76.28(n)    U74761.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5689731 nocturnin-like 64.35(n)
    67.13(a)
      568973  XM_692334.4  XP_697426.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta nocturin3
    cu1
    curled1 48(a)3
    55.19(n)1
    52.9(a)1
      86D93
    413391  NM_001104276.11  NP_001097746.11 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G315306
    AT1G315006
    carbon catabolite repressor protein 4-like 4
    24(a)
    20(a)
    possible ortholog
    possible ortholog
    1(11281188-11282468)
    1(11273605-11276577)
    rice
    (Oryza sativa)
    Liliopsida --
    endonuclease/exonuclease/phosphatase family domain...
    19(a)
    1 ↔ 1
    5(18783426-18787426)


    ENSEMBL Gene Tree for CCRN4L (if available)
    TreeFam Gene Tree for CCRN4L (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CCRN4L gene
    ANGEL12  PDE122  CNOT6L2  ANGEL22  CNOT62  

    CCRN4L for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for CCRN4L
    PGOHUM00000242901


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for CCRN4L
         1 CNV: 98901
         2 Indels: 27468 46523
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CCRN4L
    DNA2.0 Custom Variant and Variant Library Synthesis for CCRN4L

    (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.)
    About This Section

    CCRN4L for disorders           About GeneDecksing

    OMIM gene information: 608468    OMIM disorders: --

    2 diseases for CCRN4L:    About MalaCards
    lung cancer    retinitis

    Human Genome Epidemiology (HuGE) Navigator: CCRN4L (4 documents)

    Export disorders for CCRN4L 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)
    About This Section

    PubMed articles for CCRN4L gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with CCRN4L)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of a mammalian gene related to the yeast CCR4 general transcription factor and revealed by transposon insertion. (PubMed id 10521507)1, 2, 3, 9 Dupressoir A.... Heidmann T. (1999)
    2. CLOCK/BMAL1 regulates human nocturnin transcription through binding to the E-box of nocturnin promoter. (PubMed id 18587630)1, 9 Li R....Cao J.M. (2008)
    3. Rhythmic expression of Nocturnin mRNA in multiple tissues of the mouse. (PubMed id 11394964)1, 9 Wang Y....Besharse J.C. (2001)
    4. RNA processing and modification protein, carbon catabo lite repression 4 (Ccr4), arrests the cell cycle through p21-dependent and p53-i ndependent pathway. (PubMed id 22547059)1 Yi X....Shang Y. (2012)
    5. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1 Bailey S.D....Anand S. (2010)
    6. Gene-centric association signals for lipids and apoli poproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (2009)
    7. RANKL-induced CCL22/macrophage-derived chemokine produced from osteoclasts potentially promotes the bone metastasis of lung cancer expressing its receptor CCR4. (PubMed id 16821125)1 Nakamura E.S....Saiki I. (2006)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    10. Circadian regulation of nocturnin transcription by phosphorylated CREB in Xenopus retinal photoreceptor cells. (PubMed id 12370297)9 Liu X. and Green C.B. (2002)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 25819 HGNC: 14254 AceView: CCRN4L Ensembl:ENSG00000151014 euGenes: HUgn25819
    ECgene: CCRN4L H-InvDB: CCRN4L

    (According to HUGE)
    About This Section
      --

    (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 CCRN4L Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for CCRN4L gene:
    Search GeneIP for patents involving CCRN4L

    GeneCards and IP:
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