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

CGREF1 Gene

protein-coding   GIFtS: 49
GCID: GC02M027321

Cell Growth Regulator With EF-Hand Domain 1

  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
Cell Growth Regulator With EF-Hand Domain 11 2     Cell Growth Regulator With EF Hand Domain Protein 12
Cell Growth Regulatory Gene 11 Protein2 3     hydrophobestin2
CGR112 3     Hydrophobestin3
Cell Growth Regulator With EF Hand Domain 12     

External Ids:    HGNC: 169621   Entrez Gene: 106692   Ensembl: ENSG000001380287   OMIM: 6061375   UniProtKB: Q996743   

Export aliases for CGREF1 gene to outside databases

Previous GC identifers: GC02M027280 GC02M027298 GC02M027235 GC02M027176 GC02M027064


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

GeneCards Summary for CGREF1 Gene: 
CGREF1 (cell growth regulator with EF-hand domain 1) is a protein-coding gene. Diseases associated with CGREF1 include dermatitis herpetiformis, and dermatitis. GO annotations related to this gene include calcium ion binding.

UniProtKB/Swiss-Prot: CGRE1_HUMAN, Q99674
Function: Mediates cell-cell adhesion in a calcium-dependent manner (By similarity). Able to inhibit growth in
several cell lines




(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_000002.11  NT_022184.15  NC_018913.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CGREF1 gene promoter:
         Nkx2-2   AP-2gamma   LCR-F1   HNF-4alpha1   AREB6   HEN1   STAT3   AP-2beta   AP-2alpha   AP-2alphaA   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for CGREF1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CGREF1


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

Entrez Gene cytogenetic band: 2p23.3   Ensembl cytogenetic band:  2p23.3   HGNC cytogenetic band: 2p23.3

CGREF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CGREF1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M027321:  view genomic region     (about GC identifiers)

Start:
27,321,757 bp from pter      End:
27,341,995 bp from pter
Size:
20,239 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: CGRE1_HUMAN, Q99674 (See protein sequence)
Recommended Name: Cell growth regulator with EF hand domain protein 1 precursor  
Size: 301 amino acids; 31905 Da
Subcellular location: Secreted (By similarity)
Secondary accessions: A6NHV7 B4DXY8 B5MCB7 B5MCC9 B5MCP5 E7EU99 Q8N4B7
Alternative splicing: 5 isoforms:  Q99674-1   Q99674-2   Q99674-3   Q99674-4   Q99674-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CGREF1: NX_Q99674

Explore proteomics data for CGREF1 at MOPED 

Post-translational modifications:

  • UniProtKB: Probably digested extracellularly by an unknown serine protease generating extremely hydrophobic bioactive
    peptides (By similarity)
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q99674

  • CGREF1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CGREF1 Protein Expression
    REFSEQ proteins (4 alternative transcripts): 
    NP_001159711.1  NP_001159712.1  NP_001159713.1  NP_006560.3  

    ENSEMBL proteins: 
     ENSP00000394306   ENSP00000385103   ENSP00000385452   ENSP00000386113   ENSP00000324025  
     ENSP00000385574   ENSP00000395042   ENSP00000260595  

    Human Recombinant Protein Products for CGREF1: 
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    Sino Biological Recombinant Protein for CGREF1
    Sino Biological Cell Lysate for CGREF1 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for CGREF1 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    CGREF1 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
    HGNC Gene Families: 
    EFHAND: EF-hand domain containing

    3 InterPro protein domains:
     IPR011992 EF-hand-like_dom
     IPR002048 EF_hand_dom
     IPR018247 EF_Hand_1_Ca_BS

    Graphical View of Domain Structure for InterPro Entry Q99674

    ProtoNet protein and cluster: Q99674

    UniProtKB/Swiss-Prot: CGRE1_HUMAN, Q99674
    Domain: Both EF-hands are required for function (By similarity)
    Similarity: Contains 2 EF-hand domains


    CGREF1 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:

         UniProtKB/Swiss-Prot Summary: CGRE1_HUMAN, Q99674
    Function: Mediates cell-cell adhesion in a calcium-dependent manner (By similarity). Able to inhibit growth in
    several cell lines
    Induction: By p53/TP53

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    CGREF1 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for CGREF1:
     Decreased number of cells in m 

    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidCGREF1 3' UTR sequence
    Inhib. RNA
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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:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CGREF1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006950response to stress TAS8968090
    GO:0007050cell cycle arrest IEA--
    GO:0007155cell adhesion IEA--
    GO:0008285negative regulation of cell proliferation TAS8968090
    GO:0030308negative regulation of cell growth IEA--

    CGREF1 for ontologies           About GeneDecksing



    (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 CGREF1 (CGRE1)

    Search CenterWatch for drugs/clinical trials and news about CGREF1 / CGRE1

    (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 CGREF1 gene (4 alternative transcripts): 
    NM_001166239.1  NM_001166240.1  NM_001166241.1  NM_006569.5  

    Unigene Cluster for CGREF1:

    Cell growth regulator with EF-hand domain 1
    Hs.159525  [show with all ESTs]
    Unigene Representative Sequence: NM_006569
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000440612 ENST00000402550(uc021vez.1) ENST00000402394(uc002riq.3 uc021vfa.1 uc002rir.2)
    ENST00000405600(uc010eys.2) ENST00000312734 ENST00000404694(uc010eyr.2)
    ENST00000467539 ENST00000452318(uc010ylf.2) ENST00000260595
    miRNA
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    5 QIAGEN miScript miRNA Assays for microRNAs that regulate CGREF1:
    hsa-miR-125a-5p hsa-miR-670 hsa-miR-125b hsa-miR-558 hsa-miR-4319
    SwitchGear 3'UTR luciferase reporter plasmidCGREF1 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AK290128.1 AK302185.1 AK309147.1 BC034764.1 U66468.1 

    7 DOTS entries:

    DT.95104790  DT.447396  DT.447395  DT.100773249  DT.97851257  DT.121007671  DT.97846451 

    24/66 AceView cDNA sequences (see all 66):

    BM711657 CR593274 BM849276 CR623121 BQ446998 BM673850 AA325461 BM785106 
    CR619230 BX386971 Z41432 NM_006569 AL536349 AA523890 T31049 AI880122 
    BI762635 BM738764 BC034764 BU558202 BM723747 AU141077 BF063291 AW071890 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for CGREF1    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6
    SP1:                                                
    SP2:                                                


    ECgene alternative splicing isoforms for CGREF1

    (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

    CGREF1 expression in normal human tissues (normalized intensities)      CGREF1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGGGCATTT
    CGREF1 Expression
    About this image


    CGREF1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/8 selected tissues (see all 8) fully expand
     
     Kidney (Urinary System)    fully expand to see all 8 entries
             Proximal Tubule Cells Proximal Tubule
             Proximal Tubule
             visceral organ/metanephros/renal medulla   
     
     Bone (Muscoskeletal System)    fully expand to see all 6 entries
             Chondrocytes Zeugopod Epiphyseal End
             Thoracic Rib
             skeleton/pectoral girdle and thoracic body wall/scapula   
     
     Lower Urinary Tract (Urinary System)    fully expand to see all 5 entries
             visceral organ   
     
     Cartilage (Muscoskeletal System)    fully expand to see all 3 entries
             Chondrocytes Zeugopod Epiphyseal End
             skeleton/cranium/viscerocranium   
     
     Neural Crest (Gastrulation Derivatives)    fully expand to see all 2 entries
             skeleton/cranium/viscerocranium   

    See CGREF1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CGREF1

    SOURCE GeneReport for Unigene cluster: Hs.159525
        SABiosciences Custom PCR Arrays for CGREF1
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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 chordates.

    Orthologs for CGREF1 gene from 2/7 species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cgref11 , 5 cell growth regulator with EF hand domain 11, 5 75.15(n)1
    67.9(a)1
      5 (16.90 cM)5
    685671  NM_026770.11  NP_081046.11 
     309331465 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5595761 uncharacterized LOC559576 47.33(n)
    35(a)
      559576  XM_682932.5  XP_688024.3 


    ENSEMBL Gene Tree for CGREF1 (if available)
    TreeFam Gene Tree for CGREF1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    10/460 SNPs in CGREF1 are shown (see all 460)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1132338391,2
    C,F--27324216(+) TGTTTC/TCCCTG 6 K E mis1 int12Minor allele frequency- T:0.00CSA NA 4554
    rs1405169901,2
    C,F--27324222(+) CCCTGG/TAAGTT 6 T P mis1 int11Minor allele frequency- T:0.00NA 4552
    rs118934271,2
    C,F,H--27324340(+) GGCCCG/AGGGGC 6 /P syn1 int1 ese33Minor allele frequency- A:0.50NA 8
    rs10573911,2
    C,F,H--27324354(-) AGGCTG/AAAGGA 6 /K /E mis1 int1 ese33Minor allele frequency- A:0.50NA WA 8
    rs10573891,2,4
    C,F,H--27324371(-) AGCTGG/AGGGCC 6 /E /G mis1 int12Minor allele frequency- A:0.33NA 6
    rs770047461,2
    C,F--27324391(+) GGCCCA/GGGGGC 6 P syn1 int11Minor allele frequency- G:0.00NA 4002
    rs118898311,2,4
    C,F,H--27324403(+) TCTCCT/ATTAGC 6 /K /N mis1 int1 ese36Minor allele frequency- A:0.01NS EA NA 422
    rs118898321,2
    C,F,H--27324405(+) TCCTTT/CAGCCT 6 /K /E mis1 int1 ese33Minor allele frequency- C:0.08NS NA 78
    rs1386160601,2
    F--27324418(+) GCCTGG/ACCCTC 6 /G syn1 int11Minor allele frequency- A:0.00NA 3912
    rs118934781,2,4
    C,H--27324464(+) CCTCTG/ACCTGG 6 /A /V mis1 int1 ese34Minor allele frequency- A:0.00NS EA 406

    HapMap Linkage Disequilibrium report for CGREF1 (27321757 - 27341995 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for CGREF1:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv989926CNV Deletion20482838
    esv2673470CNV Deletion23128226
    esv2719833CNV Deletion23290073
    esv1742991CNV Deletion17803354
    esv2719834CNV Deletion23290073
    nsv873753CNV Loss21882294
    nsv833603CNV Loss17160897
    nsv455974CNV Loss19166990
    nsv817673CNV Gain17921354

    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for CGREF1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 606137    OMIM disorders: --

    3 diseases for CGREF1:    About MalaCards
    dermatitis herpetiformis    dermatitis    gastric cancer

    1 disease from the University of Copenhagen DISEASES database for CGREF1:
    Dermatitis herpetiformis

    CGREF1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): CGREF1
    Human Genome Epidemiology (HuGE) Navigator: CGREF1 (3 documents)

    Export disorders for CGREF1 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 CGREF1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with CGREF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Induction of cell growth regulatory genes by p53. (PubMed id 8968090)1, 2, 3 Madden S.L.... Beaudry G.A. (1996)
    2. 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, 4 Bailey S.D....Anand S. (2010)
    3. Gene-centric association signals for lipids and apoli poproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (2009)
    4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)
    6. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H....Kim N.S. (2005)
    7. 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)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (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. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 10669 HGNC: 16962 AceView: CGREF1 Ensembl:ENSG00000138028 euGenes: HUgn10669
    ECgene: CGREF1 H-InvDB: CGREF1

    (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 CGREF1 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 CGREF1 gene:
    Search GeneIP for patents involving CGREF1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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