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CELF2 (CUGBP, Elav-like family member 2)

Written2014-05Satish Ramalingam, Shrikant Anant
Department of Molecular, Integrative Physiology, Kansas University Medical Center, Kansas City, KS, USA

Abstract CELF2 belongs to the family of RNA binding proteins implicated in mRNA splicing, editing, stability and translation. This gene is encoded in a single large gene spanning over 159 kilo bases located on chromosome 10 p13-p14 (between D10S547 and D10S223). This gene has 14 transcripts (splice variants) and the 3 major splice variants have distinct exon 1. This is an evolutionarily conserved ubiquitously expressed protein. The members of the CELF protein family contain two N-terminal RNA recognition motif (RRM) domains and one C-terminal RRM domain, and a divergent segment of 160-230 amino acids between second and third RRM domains. This divergent domain is unique to CELF2 proteins and has been shown to contain one or more activation molecules required for splicing activity. CELF2 has been shown to bind to the CUG and Au-rich element (ARE) in the target mRNA and shown to be implicated in muscular dystrophy and cancer.

Keywords RNA binding protein, mRNA stability, splicing, apoptosis, translation inhibition, muscular dystrophy, cancer

(Note : for Links provided by Atlas : click)

Identity

Alias_namesCUGBP2
CUG triplet repeat, RNA-binding protein 2
CUG triplet repeat, RNA binding protein 2
Alias_symbol (synonym)Etr-3
NAPOR-2
BRUNOL3
HGNC (Hugo) CELF2
LocusID (NCBI) 10659
Atlas_Id 52815
Location 10p14  [Link to chromosome band 10p14]
Location_base_pair Starts at 11206993 and ends at 11378672 bp from pter ( according to hg19-Feb_2009)  [Mapping CELF2.png]
Fusion genes
(updated 2016)
ARHGEF1 (19q13.2) / CELF2 (10p14)CELF2 (10p14) / AARSD1 (17q21.31)CELF2 (10p14) / AHCYL2 (7q32.1)
CELF2 (10p14) / CCNH (5q14.3)CELF2 (10p14) / CELF2 (10p14)CELF2 (10p14) / LRFN1 (19q13.2)
CELF2 (10p14) / NBEA (13q13.3)CELF2 (10p14) / PTPRG (3p14.2)CELF2 (10p14) / RARA (17q21.2)
CELF2 (10p14) / WDR3 (1p12)GNAQ (9q21.2) / CELF2 (10p14)MCAM (11q23.3) / CELF2 (10p14)
SIRT1 (10q21.3) / CELF2 (10p14)TMEM158 (3p21.31) / CELF2 (10p14)
Note Size: 331416 bases. Orientation: plus strand.
This gene is encoded by a gene located on chromosome 10p13-p14 between Généthon markers D10S547 and D10S223 (Li et al., 2001).

DNA/RNA

Description The human CELF2 gene contains 14 exons spanning over approximately 159 kb of the genomic DNA.
Transcription Alternative promoters usage of CELF2 gene results in three transcript variants, where the variants 2 and 3 proteins have distinct exon 1 resulting in different 5' untranslated region (UTR) and have extended N-terminal sequences (Ramalingam et al., 2008). There are totally 14 transcripts (splice variants) reported so far.

Protein

 
  Figure 1. RRM position of CELF2 protein variants.
Description This is an evolutionarily conserved protein. The members of the CELF protein family contain two N-terminal RNA recognition motif (RRM) domains and one C-terminal RRM domain, and a divergent segment of 160-230 amino acids between second and third RRM domains. This divergent domain is unique to CELF2 proteins and has been shown to contain one or more activation molecules required for splicing activity (figure 1).
Expression CELF2 is a ubiquitously expressed protein. According to the NCBI Entrez GEO profiles the CELF2 is expressed in brain, heart, thymus, spleen, bone, tongue, stomach, intestine, pancreas, liver, breast, lung, kidney, testis, ovary, prostate, placenta and skin. In addition, according to expression atlas brain, bone marrow, heart, spleen, lymph node, ovary and adipose tissue has more expression of CELF2.
Localisation CELF2 variant 1 is predominantly nuclear, while variants 2 and 3 are predominantly cytoplasmic (Ramalingam et al., 2008). CELF2 variant 1 accumulates in the cytoplasm following radiation exposure (Mukhopadhyay et al., 2003a). The C terminus of CELF2 transcript variant 1 is rich in arginine and lysine residues 13 amino acids (KRLKVQLKRSKND) 467 - 480, which is common for NLS elements recognized by importin proteins. Ladd and Cooper, has reported that the C-terminus of CELF2 contains a strong nuclear localization signal overlapping the third RRM (Ladd and Cooper, 2004). However, our unpublished data suggests that nuclear localization signal extends to the RNA recognition motif 1 and 2 domains. Finally, CELF2 has several leucine-rich motifs that resembles nuclear export signals recognized by the export protein CRM1.
Function CELF2 is an RNA-binding protein implicated in the regulation of several post-transcriptional events. It has been shown to regulate pre-mRNA splicing (Faustino and Cooper, 2005), mRNA editing (Anant et al., 2001), mRNA translation and stability. CELF2 has been shown to be involved in alternative splicing of muscle specific genes including exon 5 of cardiac troponin T (Ladd et al., 2001), exon 11 of insulin receptor, intron 2 of chloride channel 1, exons 5 and 21 of NMDAR-1, and the muscle-specific exon of α-actinin (Gromak et al., 2003). Another function for CELF2 relates to its ability to bind to AU-rich sequences in 3' untranslated region (3' UTR) of the target mRNAs. Upon binding to the AU-rich sequences in cyclooxygenase-2 (COX-2) 3' UTR, CELF2 enhances the stability of COX-2 mRNA. However, CUGBP2 binding also results in the inhibition of its translation (Murmu et al., 2004). In our earlier studies we have demonstrated that CELF2 can interact with HuR, a key inducer of RNA stability and translation, and competitively inhibit HuR function (Sureban et al., 2007). Recently, platelet derived growth factor was shown to enhance CELF2 binding to COX-2 mRNA through increased phosphorylation of a tyrosine residue at position 39 in the protein (Xu et al., 2007). These data suggest that posttranscriptional control mechanisms are in place to modulate the CELF2 function as a regulator of stability and translation of AU-rich transcripts.
Homology According to GeneCards, the CELF2 has orthologs in 72 species including much lower organisms such as Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, Xenopus tropicalis and Oryza sativa. Furthermore, in humans it has 6 paralogs from CELF1 to CELF6.

Mutations

Note According to GeneCards, there is 7518 single nucleotide polymorphism. However, Ensembl reports that CELF2 has 7768 SNPs. In addition, the Database of Genomic Variants shows that CELF2 has 18 structural variations.

Implicated in

Note
  
Entity Colon cancer
Note Putative tumor suppressor CELF2 expression is consistently reduced during neoplastic transformation suggesting that it might play a crucial role in tumor initiation and progression of colon cancer. In addition, CELF2 has been shown to induce mitotic catastrophic cell death in colon cancer (Ramalingam et al., 2012).
  
  
Entity Pancreatic cancer
Note Curcumin inhibits the pancreatic cancer growth by inducing the expression of CELF2 thereby regulating the levels of cyclooxygenase 2 and vascular endothelial growth factor expression (Subramaniam et al., 2011).
  
  
Entity Breast cancer
Note Breast cancer cells underwent apoptotic cell death in response to radiation injury and this was reversed by knockdown of CELF2 using specific siRNA (Mukhopadhyay et al., 2003b).
  
  
Entity Neuroblastoma
Note Colchicine treatment of neuroblastoma cells resulted in apoptotic cell death and CELF2 has been shown to be involved in the process of cell death (Li et al., 2001).
  
  
Entity Alzheimer's disease
Note It has been shown that variants in CUGBP2 on chromosome 10p, are associated with AD in those highest-risk APOE e4 homozygotes. This interaction observation is replicated in independent samples. CELF2 has one isoform that is expressed predominantly in neurons, and identification of such a new risk locus is important because of the severity of AD (Wijsman et al., 2011).
  
  
Entity Heart disease
Note Arrhythmogenic right ventricular dysplasia is the most common cause of sudden cardiac death in the young in Italy and the second most common cause in the United States. One of the genes that was mapped to this is in the vicinity of chromosome 10p12-p14 and it is CELF2 (Li et al., 2001).
  
  
Entity Ischemia
Note The transient global ischemia induces the translational inhibition of genes with increased expression in normothermic mice. The author's correlate the translational inhibition with CELF2 expression and this might play an important role in the progress of neuronal injury after transient global ischemia (Otsuka et al., 2009).
  
  
Entity Atrophy
Note The differential expression of CELF2 has been confirmed with real-time RT-PCR in spinal cord and muscle of three different models of spinal muscular atrophy (Anderson et al., 2004). Spinal and bulbar muscular atrophy (SBMA) is an inherited neurodegenerative disorder caused by the expansion of the polyglutamine (polyQ) tract of the androgen receptor (AR-polyQ). It has been shown that miR-196a enhanced the decay of the AR mRNA by silencing CUGBP, Elav-like family member 2 (CELF2). CELF2 shown to directly act on AR mRNA and enhance the stability of AR mRNA (Miyazaki et al., 2012). Myotonic dystrophy (DM) is a neuromuscular disorder associated with CTG triplet repeat expansion in the myotonin protein kinase gene (DMPK). It has been suggested that the expanded CUG repeats sequester specific RNA-binding proteins and that such a sequestration results in abnormal RNA processing of several RNAs containing CUG repeats in multiple tissues affected in patients with DM. One of the members of the CUG-binding proteins, CUG-BP, has been identified previously (Lu et al., 1999).
  
  
Entity Development
Note Overexpression of CELF2 by RNA microinjection resulted in severe defects in nervous system and gastrulation, suggesting the need for tight control of napor gene regulation during embryo development (Choi et al., 2003). CELF2 appears to be an important factor for thymus development and is therefore a candidate gene for the thymus hypoplasia/aplasia seen in partial monosomy 10p patients (Lichtner et al., 2002).
  

Bibliography

Novel role for RNA-binding protein CUGBP2 in mammalian RNA editing. CUGBP2 modulates C to U editing of apolipoprotein B mRNA by interacting with apobec-1 and ACF, the apobec-1 complementation factor.
Anant S, Henderson JO, Mukhopadhyay D, Navaratnam N, Kennedy S, Min J, Davidson NO.
J Biol Chem. 2001 Dec 14;276(50):47338-51. Epub 2001 Sep 27.
PMID 11577082
 
Expression profiling in spinal muscular atrophy reveals an RNA binding protein deficit.
Anderson KN, Baban D, Oliver PL, Potter A, Davies KE.
Neuromuscul Disord. 2004 Nov;14(11):711-22.
PMID 15482955
 
Isolation and expression of Napor/CUG-BP2 in embryo development.
Choi DK, Yoo KW, Hong SK, Rhee M, Sakaki Y, Kim CH.
Biochem Biophys Res Commun. 2003 Jun 6;305(3):448-54.
PMID 12763013
 
Identification of putative new splicing targets for ETR-3 using sequences identified by systematic evolution of ligands by exponential enrichment.
Faustino NA, Cooper TA.
Mol Cell Biol. 2005 Feb;25(3):879-87.
PMID 15657417
 
Antagonistic regulation of alpha-actinin alternative splicing by CELF proteins and polypyrimidine tract binding protein.
Gromak N, Matlin AJ, Cooper TA, Smith CW.
RNA. 2003 Apr;9(4):443-56.
PMID 12649496
 
The CELF family of RNA binding proteins is implicated in cell-specific and developmentally regulated alternative splicing.
Ladd AN, Charlet N, Cooper TA.
Mol Cell Biol. 2001 Feb;21(4):1285-96.
PMID 11158314
 
Multiple domains control the subcellular localization and activity of ETR-3, a regulator of nuclear and cytoplasmic RNA processing events.
Ladd AN, Cooper TA.
J Cell Sci. 2004 Jul 15;117(Pt 16):3519-29. Epub 2004 Jun 29.
PMID 15226369
 
Genomic organization and isoform-specific tissue expression of human NAPOR (CUGBP2) as a candidate gene for familial arrhythmogenic right ventricular dysplasia.
Li D, Bachinski LL, Roberts R.
Genomics. 2001 Jun 15;74(3):396-401.
PMID 11414768
 
Expression and mutation analysis of BRUNOL3, a candidate gene for heart and thymus developmental defects associated with partial monosomy 10p.
Lichtner P, Attie-Bitach T, Schuffenhauer S, Henwood J, Bouvagnet P, Scambler PJ, Meitinger T, Vekemans M.
J Mol Med (Berl). 2002 Jul;80(7):431-42. Epub 2002 Apr 4.
PMID 12110949
 
Cardiac elav-type RNA-binding protein (ETR-3) binds to RNA CUG repeats expanded in myotonic dystrophy.
Lu X, Timchenko NA, Timchenko LT.
Hum Mol Genet. 1999 Jan;8(1):53-60.
PMID 9887331
 
Viral delivery of miR-196a ameliorates the SBMA phenotype via the silencing of CELF2.
Miyazaki Y, Adachi H, Katsuno M, Minamiyama M, Jiang YM, Huang Z, Doi H, Matsumoto S, Kondo N, Iida M, Tohnai G, Tanaka F, Muramatsu S, Sobue G.
Nat Med. 2012 Jul;18(7):1136-41. doi: 10.1038/nm.2791.
PMID 22660636
 
CUGBP2 plays a critical role in apoptosis of breast cancer cells in response to genotoxic injury.
Mukhopadhyay D, Jung J, Murmu N, Houchen CW, Dieckgraefe BK, Anant S.
Ann N Y Acad Sci. 2003b Dec;1010:504-9.
PMID 15033780
 
Dynamic antagonism between RNA-binding protein CUGBP2 and cyclooxygenase-2-mediated prostaglandin E2 in radiation damage.
Murmu N, Jung J, Mukhopadhyay D, Houchen CW, Riehl TE, Stenson WF, Morrison AR, Arumugam T, Dieckgraefe BK, Anant S.
Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13873-8. Epub 2004 Sep 9.
PMID 15358864
 
Transcriptional induction and translational inhibition of Arc and Cugbp2 in mice hippocampus after transient global ischemia under normothermic condition.
Otsuka N, Tsuritani K, Sakurai T, Kato K, Matoba R, Itoh J, Okuyama S, Yamada K, Yoneda Y.
Brain Res. 2009 Sep 1;1287:136-45. doi: 10.1016/j.brainres.2009.06.050. Epub 2009 Jun 24.
PMID 19559013
 
Reduced Expression of RNA Binding Protein CELF2, a Putative Tumor Suppressor Gene in Colon Cancer.
Ramalingam S, Ramamoorthy P, Subramaniam D, Anant S.
Immunogastroenterology. 2012;1(1):27-33.
PMID 23795348
 
RNA binding protein CUGBP2/CELF2 mediates curcumin-induced mitotic catastrophe of pancreatic cancer cells.
Subramaniam D, Ramalingam S, Linehan DC, Dieckgraefe BK, Postier RG, Houchen CW, Jensen RA, Anant S.
PLoS One. 2011 Feb 11;6(2):e16958. doi: 10.1371/journal.pone.0016958.
PMID 21347286
 
Functional antagonism between RNA binding proteins HuR and CUGBP2 determines the fate of COX-2 mRNA translation.
Sureban SM, Murmu N, Rodriguez P, May R, Maheshwari R, Dieckgraefe BK, Houchen CW, Anant S.
Gastroenterology. 2007 Mar;132(3):1055-65. Epub 2006 Dec 19.
PMID 17383427
 
Genome-wide association of familial late-onset Alzheimer's disease replicates BIN1 and CLU and nominates CUGBP2 in interaction with APOE.
Wijsman EM, Pankratz ND, Choi Y, Rothstein JH, Faber KM, Cheng R, Lee JH, Bird TD, Bennett DA, Diaz-Arrastia R, Goate AM, Farlow M, Ghetti B, Sweet RA, Foroud TM, Mayeux R; NIA-LOAD/NCRAD Family Study Group.
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PMID 21379329
 
Platelet-derived growth factor-induced stabilization of cyclooxygenase 2 mRNA in rat smooth muscle cells requires the c-Src family of protein-tyrosine kinases.
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Citation

This paper should be referenced as such :
S Ramalingam, S Anant
CELF2 (CUGBP, Elav-like family member 2)
Atlas Genet Cytogenet Oncol Haematol. 2015;19(2):93-96.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/CELF2ID52815ch10p14.html


External links

Nomenclature
HGNC (Hugo)CELF2   2550
Cards
AtlasCELF2ID52815ch10p14
Entrez_Gene (NCBI)CELF2  10659  CUGBP, Elav-like family member 2
AliasesBRUNOL3; CUGBP2; ETR-3; ETR3; 
NAPOR
GeneCards (Weizmann)CELF2
Ensembl hg19 (Hinxton)ENSG00000048740 [Gene_View]  chr10:11206993-11378672 [Contig_View]  CELF2 [Vega]
Ensembl hg38 (Hinxton)ENSG00000048740 [Gene_View]  chr10:11206993-11378672 [Contig_View]  CELF2 [Vega]
ICGC DataPortalENSG00000048740
TCGA cBioPortalCELF2
AceView (NCBI)CELF2
Genatlas (Paris)CELF2
WikiGenes10659
SOURCE (Princeton)CELF2
Genetics Home Reference (NIH)CELF2
Genomic and cartography
GoldenPath hg19 (UCSC)CELF2  -     chr10:11206993-11378672 +  10p13   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)CELF2  -     10p13   [Description]    (hg38-Dec_2013)
EnsemblCELF2 - 10p13 [CytoView hg19]  CELF2 - 10p13 [CytoView hg38]
Mapping of homologs : NCBICELF2 [Mapview hg19]  CELF2 [Mapview hg38]
OMIM602538   
Gene and transcription
Genbank (Entrez)AA595891 AF036956 AF086447 AF090693 AF090694
RefSeq transcript (Entrez)NM_001025076 NM_001025077 NM_001083591 NM_006561
RefSeq genomic (Entrez)NC_000010 NC_018921 NT_008705 NW_004929370
Consensus coding sequences : CCDS (NCBI)CELF2
Cluster EST : UnigeneHs.309288 [ NCBI ]
CGAP (NCI)Hs.309288
Alternative Splicing GalleryENSG00000048740
Gene ExpressionCELF2 [ NCBI-GEO ]   CELF2 [ EBI - ARRAY_EXPRESS ]   CELF2 [ SEEK ]   CELF2 [ MEM ]
Gene Expression Viewer (FireBrowse)CELF2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10659
GTEX Portal (Tissue expression)CELF2
Protein : pattern, domain, 3D structure
UniProt/SwissProtO95319   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO95319  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO95319
Splice isoforms : SwissVarO95319
PhosPhoSitePlusO95319
Domaine pattern : Prosite (Expaxy)RRM (PS50102)   
Domains : Interpro (EBI)Hud_Sxl_RNA    Nucleotide-bd_a/b_plait    RRM_dom   
Domain families : Pfam (Sanger)RRM_1 (PF00076)   
Domain families : Pfam (NCBI)pfam00076   
Domain families : Smart (EMBL)RRM (SM00360)  
Conserved Domain (NCBI)CELF2
DMDM Disease mutations10659
Blocks (Seattle)CELF2
PDB (SRS)2MY7    2MY8    4LJM    4LMZ    4TLQ   
PDB (PDBSum)2MY7    2MY8    4LJM    4LMZ    4TLQ   
PDB (IMB)2MY7    2MY8    4LJM    4LMZ    4TLQ   
PDB (RSDB)2MY7    2MY8    4LJM    4LMZ    4TLQ   
Structural Biology KnowledgeBase2MY7    2MY8    4LJM    4LMZ    4TLQ   
SCOP (Structural Classification of Proteins)2MY7    2MY8    4LJM    4LMZ    4TLQ   
CATH (Classification of proteins structures)2MY7    2MY8    4LJM    4LMZ    4TLQ   
SuperfamilyO95319
Human Protein AtlasENSG00000048740
Peptide AtlasO95319
HPRD03964
IPIIPI00845480   IPI00607544   IPI00410277   IPI00853320   IPI01011300   IPI00910773   IPI01012672   IPI00845479   
Protein Interaction databases
DIP (DOE-UCLA)O95319
IntAct (EBI)O95319
FunCoupENSG00000048740
BioGRIDCELF2
STRING (EMBL)CELF2
ZODIACCELF2
Ontologies - Pathways
QuickGOO95319
Ontology : AmiGOnucleotide binding  RNA binding  nucleus  cytoplasm  RNA processing  mRNA processing  regulation of heart contraction  poly(A) RNA binding  
Ontology : EGO-EBInucleotide binding  RNA binding  nucleus  cytoplasm  RNA processing  mRNA processing  regulation of heart contraction  poly(A) RNA binding  
NDEx NetworkCELF2
Atlas of Cancer Signalling NetworkCELF2
Wikipedia pathwaysCELF2
Orthology - Evolution
OrthoDB10659
GeneTree (enSembl)ENSG00000048740
Phylogenetic Trees/Animal Genes : TreeFamCELF2
HOVERGENO95319
HOGENOMO95319
Homologs : HomoloGeneCELF2
Homology/Alignments : Family Browser (UCSC)CELF2
Gene fusions - Rearrangements
Fusion : MitelmanSIRT1/CELF2 [10q21.3/10p14]  [t(10;10)(p14;q21)]  
Fusion: TCGASIRT1 10q21.3 CELF2 10p14 LUAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCELF2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CELF2
dbVarCELF2
ClinVarCELF2
1000_GenomesCELF2 
Exome Variant ServerCELF2
ExAC (Exome Aggregation Consortium)CELF2 (select the gene name)
Genetic variants : HAPMAP10659
Genomic Variants (DGV)CELF2 [DGVbeta]
DECIPHER (Syndromes)10:11206993-11378672  ENSG00000048740
CONAN: Copy Number AnalysisCELF2 
Mutations
ICGC Data PortalCELF2 
TCGA Data PortalCELF2 
Broad Tumor PortalCELF2
OASIS PortalCELF2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCELF2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCELF2
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch CELF2
DgiDB (Drug Gene Interaction Database)CELF2
DoCM (Curated mutations)CELF2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CELF2 (select a term)
intoGenCELF2
NCG5 (London)CELF2
Cancer3DCELF2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602538   
Orphanet
MedgenCELF2
Genetic Testing Registry CELF2
NextProtO95319 [Medical]
TSGene10659
GENETestsCELF2
Huge Navigator CELF2 [HugePedia]
snp3D : Map Gene to Disease10659
BioCentury BCIQCELF2
ClinGenCELF2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD10659
Chemical/Pharm GKB GenePA27046
Clinical trialCELF2
Miscellaneous
canSAR (ICR)CELF2 (select the gene name)
Probes
Litterature
PubMed45 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCELF2
EVEXCELF2
GoPubMedCELF2
iHOPCELF2
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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