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LOH12CR1 Gene

protein-coding   GIFtS: 44
GCID: GC12P012510

Loss Of Heterozygosity, 12, Chromosomal Region 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)
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Aliases
Loss Of Heterozygosity, 12, Chromosomal Region 11 2
LOH1CR122
Loss Of Heterozygosity 12 Chromosomal Region 1 Protein2

External Ids:    HGNC: 179501   Entrez Gene: 1184262   Ensembl: ENSG000001657147   UniProtKB: Q969J33   

Export aliases for LOH12CR1 gene to outside databases

Previous GC identifers: GC12P012238 GC12P012654 GC12P012410 GC12P012401 GC12P012276


(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 LOH12CR1 Gene:
LOH12CR1 (loss of heterozygosity, 12, chromosomal region 1) is a protein-coding gene. Diseases associated with LOH12CR1 include lymphoblastic leukemia, and inflammatory bowel disease.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the LOH12CR1 gene promoter:
         Sp1   HTF   FOXD1   LCR-F1   RORalpha1   FOXJ2 (long isoform)   c-Myb   FOXJ2   ZID   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLOH12CR1 promoter sequence
   Search Chromatin IP Primers for LOH12CR1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LOH12CR1


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

Entrez Gene cytogenetic band: 12p12   Ensembl cytogenetic band:  12p13.2   HGNC cytogenetic band: 12p12

LOH12CR1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LOH12CR1 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P012510:  view genomic region     (about GC identifiers)

Start:
12,510,013 bp from pter      End:
12,619,840 bp from pter
Size:
109,828 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: L12R1_HUMAN, Q969J3 (See protein sequence)
Recommended Name: Loss of heterozygosity 12 chromosomal region 1 protein  
Size: 196 amino acids; 22222 Da
Secondary accessions: Q96QS5
Alternative splicing: 2 isoforms:  Q969J3-1   Q969J3-2   

Explore the universe of human proteins at neXtProt for LOH12CR1: NX_Q969J3

Explore proteomics data for LOH12CR1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See LOH12CR1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_477517.1  
    ENSEMBL proteins: 
     ENSP00000443023   ENSP00000321546   ENSP00000298571  

    LOH12CR1 Human Recombinant Protein Products:

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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:
     IPR018780 Tumour_suppressor_LOH1CR12

    Graphical View of Domain Structure for InterPro Entry Q969J3

    ProtoNet protein and cluster: Q969J3

    UniProtKB/Swiss-Prot: L12R1_HUMAN, Q969J3
    Similarity: Belongs to the LOH12CR1 family


    LOH12CR1 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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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LOH12CR1
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    miRNA
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    miRTarBase miRNAs that target LOH12CR1:
    hsa-mir-335-5p (MIRT018422)

    Block miRNA regulation of human, mouse, rat LOH12CR1 using miScript Target Protectors
    1 qRT-PCR Assays for microRNA that regulate LOH12CR1:
    hsa-miR-590-3p
    SwitchGear 3'UTR luciferase reporter plasmidLOH12CR1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat LOH12CR1

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    GenScript: all cDNA clones in your preferred vector: LOH12CR1 (NM_058169)
    Sino Biological Human cDNA Clone for LOH12CR1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LOH12CR1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LOH12CR1

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LOH12CR1


    (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
    cytosol2
    nucleus2

    (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 LOH12CR1
    Interactions:

        Search GeneGlobe Interaction Network for LOH12CR1

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

    Selected Interacting proteins for LOH12CR1 (Q969J32, 3 ENSP000003215464) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PUF60Q9UHX12, 3, ENSP000003220164MINT-67107 I2D: score=4 STRING: ENSP00000322016
    MAD2L1Q132573I2D: score=5 
    UBE2L3P680363I2D: score=5 
    CSDE1O755343I2D: score=3 
    AIMP1Q129043I2D: score=2 
    About this table

    (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 LOH12CR1 (L12R1)



    (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 LOH12CR1 gene: 
    NM_058169.3  

    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000542728 ENST00000314565(uc001ral.2 uc009zhu.2) ENST00000543990
    ENST00000298571
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate LOH12CR1:
    hsa-miR-590-3p
    SwitchGear 3'UTR luciferase reporter plasmidLOH12CR1 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for LOH12CR1
    Predesigned siRNA for gene silencing in human, mouse, rat LOH12CR1
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: LOH12CR1 (NM_058169)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LOH12CR1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LOH12CR1
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for LOH12CR1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat LOH12CR1
      QuantiTect SYBR Green Assays in human, mouse, rat LOH12CR1
      QuantiFast Probe-based Assays in human, mouse, rat LOH12CR1

    Selected AceView cDNA sequences (see all 78):

    AW026232 AY037865 AW504388 CR626601 AY037866 AA256281 BI755201 AA447954 
    BF346137 AW453026 BQ690027 CB120142 BC013668 AI393641 AI341504 CK822986 
    CD635567 BQ086329 NM_058169 BQ102406 BX477004 BQ576126 CA306615 BU625021 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for LOH12CR1    About this scheme

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


    ECgene alternative splicing isoforms for LOH12CR1

    (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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    LOH12CR1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAAATCTGAC
    LOH12CR1 Expression
    About this image

    LOH12CR1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LOH12CR1 Protein Expression

    UniProtKB/Swiss-Prot: L12R1_HUMAN, Q969J3
    Tissue specificity: Widely expressed

        Custom PCR Arrays for LOH12CR1
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    QuantiFast Probe-based Assays in human, mouse, rat LOH12CR1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LOH12CR1

    (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 animals.

    Orthologs for LOH12CR1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Loh12cr11 , 5 loss of heterozygosity, 12, chromosomal region 1 homolog more1, 5 87.91(n)1
    95.85(a)1
      6 (65.77 cM)5
    677741  NM_026371.31  NP_080647.21 
     1346409405 
    chicken
    (Gallus gallus)
    Aves LOH12CR11 loss of heterozygosity, 12, chromosomal region 1 80.63(n)
    89.39(a)
      426116  NM_001031357.1  NP_001026528.1 
    lizard
    (Anolis carolinensis)
    Reptilia LOH12CR16
    loss of heterozygosity, 12, chromosomal region 1
    90(a)
    1 ↔ 1
    5(83016132-83031263)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia loh12cr11 loss of heterozygosity, 12, chromosomal region 1 74.78(n)
    82.38(a)
      100127605  NM_001112962.1  NP_001106433.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.187152 Transcribed sequence with moderate similarity to protein more 77.72(n)    CK396627.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG118021 CG11802 49.26(n)
    37.78(a)
      32145  NM_132531.2  NP_572759.1 
    worm
    (Caenorhabditis elegans)
    Secernentea F59E12.116
    Protein F59E12.11 (F59E12.11) mRNA, complete cds
    19(a)
    1 ↔ 1
    II(5647983-5649470) WBGene00019126


    ENSEMBL Gene Tree for LOH12CR1 (if available)
    TreeFam Gene Tree for LOH12CR1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    (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 LOH12CR1 (see all 2641)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs678381021,2
    C--12345313(+) TTTTC-/T/TTT 
     T
    /TTTTT
    TTTTT
    1 -- int11NA 2
    rs1863709071,2
    --12512009(+) GATATC/TTGGGG 1 -- int10--------
    rs1176697941,2
    F--12512031(+) TTCTTG/AGTCTA 1 -- int11Minor allele frequency- A:0.01EA 120
    rs752531971,2
    C--12512257(+) GCCCAA/GGAGTT 1 -- int10--------
    rs357328271,2
    C--12512299(+) TTTTT-/TGAGAC 1 -- int11Minor allele frequency- T:0.00NA 2
    rs1114708771,2
    C--12512328(+) AGTCTC/TACTGT 1 -- int11Minor allele frequency- T:0.50CSA 2
    rs1135686701,2
    C,F--12512443(+) GGGACT/ATGCCA 1 -- int11Minor allele frequency- A:0.50CSA 2
    rs1903515581,2
    --12512499(+) CCATGC/TTGGCC 1 -- int10--------
    rs1138395911,2
    C,F--12512503(+) GTTGGC/ACAGGC 1 -- int11Minor allele frequency- A:0.50CSA 2
    rs1828633371,2
    --12512531(+) CCTCAA/GGTGAT 1 -- int10--------

    HapMap Linkage Disequilibrium report for LOH12CR1 (12510013 - 12619840 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for LOH12CR1 (see all 24):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2662165CNV Deletion23128226
    esv2745568CNV Deletion23290073
    esv2421794CNV Deletion20811451
    dgv269e199CNV Deletion23128226
    esv2745567CNV Deletion23290073
    esv2673347CNV Deletion23128226
    esv271155CNV Insertion20981092
    esv274447CNV Insertion20981092
    nsv818893CNV Loss17921354
    dgv187n27CNV Loss19166990

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing LOH12CR1
    DNA2.0 Custom Variant and Variant Library Synthesis for LOH12CR1

    (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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    4 diseases for LOH12CR1:    
    About MalaCards
    lymphoblastic leukemia    inflammatory bowel disease    leukemia    malaria


    LOH12CR1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): LOH12CR1

    Export disorders for LOH12CR1 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 LOH12CR1 gene, integrated from 10 sources (see all 17):
    (articles sorted by number of sources associating them with LOH12CR1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A detailed transcriptional map of the chromosome 12p12 tumour suppressor locus. (PubMed id 11896457)1, 2, 3 Montpetit A.... Sinnett D. (Eur. J. Hum. Genet. 2002)
    2. Mutational and expression analysis of the chromosome 12p candidate tumor suppressor genes in pre-B acute lymphoblastic leukemia. (PubMed id 15284860)1, 3 Montpetit A.... Sinnett D. (Leukemia 2004)
    3. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    4. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. (PubMed id 23128233)1 Jostins L....Cho J.H. (Nature 2012)
    5. 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)
    6. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    7. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (Sci. Signal. 2011)
    8. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    9. Identification of FBXO25-interacting proteins using an integrated proteomics approach. (PubMed id 20473970)1 Teixeira F.R.... Gomes M.D. (Proteomics 2010)
    10. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. (PubMed id 19413330)2 Gauci S....Mohammed S. (Anal. Chem. 2009)

    (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: 118426 HGNC: 17950 AceView: LOH12CR1 Ensembl:ENSG00000165714 euGenes: HUgn118426
    ECgene: LOH12CR1 H-InvDB: LOH12CR1

    (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)
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    NameDescription
    PharmGKB entry for LOH12CR1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for LOH12CR1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LOH12CR1 gene:
    Search GeneIP for patents involving LOH12CR1

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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     OriGene Antibodies for LOH12CR1   OriGene RNAi products in human, mouse, rat for LOH12CR1  
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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