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AMD1 Gene

protein-coding   GIFtS: 71
GCID: GC06P111195

Adenosylmethionine Decarboxylase 1

(Previous name: S-adenosylmethionine decarboxylase 1)
  See AMD1-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
Adenosylmethionine Decarboxylase 11 2     EC 4.1.1.503 8
S-Adenosylmethionine Decarboxylase 11 2     ADOMETDC2
AMD2 3     S-Adenosylmethionine Decarboxylase Proenzyme2
SAMDC2 3     AdoMetDC3

External Ids:    HGNC: 4571   Entrez Gene: 2622   Ensembl: ENSG000001235057   OMIM: 1809805   UniProtKB: P177073   

Export aliases for AMD1 gene to outside databases

Previous GC identifers: GC06P111031 GC06P111218 GC06P111241 GC06P111304 GC06P108767


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for AMD1 Gene:
This gene encodes an important intermediate enzyme in polyamine biosynthesis. The polyamines spermine, spermidine,
and putrescine are low-molecular-weight aliphatic amines essential for cellular proliferation and tumor
promotion. Multiple alternatively spliced transcript variants have been identified. Pseudogenes of this gene are
found on chromosomes 5, 6, 10, X and Y. (provided by RefSeq, Dec 2013)

GeneCards Summary for AMD1 Gene:
AMD1 (adenosylmethionine decarboxylase 1) is a protein-coding gene. Diseases associated with AMD1 include chagas disease, and sleeping sickness. GO annotations related to this gene include adenosylmethionine decarboxylase activity.




(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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RefSeq DNA sequence at NCBI GenBank:
NC_000006.11  NC_018917.2  NT_025741.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the AMD1 gene promoter:
         SRY   FOXO4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): AMD1 promoter sequence
   Search Chromatin IP Primers for AMD1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat AMD1


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

Entrez Gene cytogenetic band: 6q21   Ensembl cytogenetic band:  6q21   HGNC cytogenetic band: 6q21

AMD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
AMD1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P111195:  view genomic region     (about GC identifiers)

Start:
111,195,973 bp from pter      End:
111,216,916 bp from pter
Size:
20,944 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: DCAM_HUMAN, P17707 (See protein sequence)
Recommended Name: S-adenosylmethionine decarboxylase proenzyme precursor  
Size: 334 amino acids; 38340 Da
Cofactor: Pyruvoyl group
Subunit: Heterotetramer of two alpha and two beta chains
Selected PDB 3D structures from and Proteopedia for AMD1 (see all 25):
1I72 (3D)        1I79 (3D)        1I7B (3D)        1I7C (3D)        1I7M (3D)        1JEN (3D)    
Secondary accessions: E1P5F7 Q5VXN4 Q5VXN6 Q9BWK4
Alternative splicing: 2 isoforms:  P17707-1   P17707-2   

Explore the universe of human proteins at neXtProt for AMD1: NX_P17707

Explore proteomics data for AMD1 at MOPED

Post-translational modifications: 

  • Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation
    process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic
    post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction,
    and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the
    proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which
    the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain,
    while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl
    group blocking the N-terminus of the alpha chain1
  • Ubiquitination2 at Lys96, Lys291, Lys301
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for AMD1 (P17707) (see all 14)
     PCGYSMN  TIHITPE  YVLSESS  VMDQFYMK 


    See AMD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001274143.1  NP_001274145.1  NP_001625.2  NP_001274144.1  

    ENSEMBL proteins: 
     ENSP00000357880   ENSP00000357877   ENSP00000357870   ENSP00000433396   ENSP00000389988  
     ENSP00000357871  
    Reactome Protein details: P17707

    AMD1 Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Protein for AMD1
    OriGene Protein Over-expression Lysate for AMD1
    OriGene MassSpec for AMD1
    OriGene Custom Protein Services for AMD1
    GenScript Custom Purified and Recombinant Proteins Services for AMD1
    Novus Biologicals AMD1 Proteins
    Novus Biologicals AMD1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    ProSpec Recombinant Protein for AMD1
    Cloud-Clone Corp. Proteins for AMD1

     
    Search eBioscience for Proteins for AMD1 

    AMD1 Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse R&D Systems for Antibodies
    OriGene Antibodies for AMD1
    OriGene Custom Antibody Services for AMD1
    Novus Biologicals AMD1 Antibodies
    Abcam antibodies for AMD1
    Cloud-Clone Corp. Antibodies for AMD1
    ThermoFisher Antibodies for AMD1
    LSBio Antibodies in human, mouse, rat for AMD1

    AMD1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for AMD1
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for AMD1
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for AMD1
    Cloud-Clone Corp. CLIAs for AMD1
    Search eBioscience for ELISAs for AMD1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    IUPHAR Guide to PHARMACOLOGY protein family classification: S-Adenosylmethionine decarboxylase
    Decarboxylases

    4 InterPro protein domains:
     IPR016067 S-AdoMet_deCO2ase_core
     IPR001985 S-AdoMet_decarboxylase
     IPR018166 S-AdoMet_deCO2ase_CS
     IPR018167 S-AdoMet_decarboxylase_subgr

    Graphical View of Domain Structure for InterPro Entry P17707

    ProtoNet protein and cluster: P17707

    1 Blocks protein domain: IPB001985 S-adenosylmethionine decarboxylase

    UniProtKB/Swiss-Prot: DCAM_HUMAN, P17707
    Similarity: Belongs to the eukaryotic AdoMetDC family


    Find genes that share domains with AMD1           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DCAM_HUMAN, P17707
    Catalytic activity: S-adenosyl-L-methionine = S-adenosyl 3-(methylthio)propylamine + CO(2)
    Enzyme regulation: Both proenzyme processing and catalytic activity are stimulated by putrescine. Catalytic
    activity is inhibited by iodoacetic acid

         Genatlas biochemistry entry for AMD1:
    S-adenosylmethionine decarboxylase 1 (Adomet DC),polyamine biosynthesis

         Enzyme Number (IUBMB): EC 4.1.1.501 2

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004014adenosylmethionine decarboxylase activity TAS1917972
         
    Find genes that share ontologies with AMD1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for AMD1:
     Increased cilium length after  

         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Amd1):
     embryogenesis  mortality/aging 

    Find genes that share phenotypes with AMD1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Amd1tm1Kiga for AMD1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for AMD1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for AMD1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for AMD1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for AMD1

    miRNA
    Products:
        
    miRTarBase miRNAs that target AMD1:
    hsa-mir-186-5p (MIRT021147), hsa-mir-324-3p (MIRT042921), hsa-mir-762 (MIRT006862), hsa-mir-17-5p (MIRT050922)

    Block miRNA regulation of human, mouse, rat AMD1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate AMD1 (see all 25):
    hsa-miR-21* hsa-miR-4288 hsa-miR-2110 hsa-miR-513a-5p hsa-miR-450a hsa-miR-632 hsa-miR-374a hsa-miR-132
    SwitchGear 3'UTR luciferase reporter plasmidAMD1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for AMD1
    Predesigned siRNA for gene silencing in human, mouse, rat AMD1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for AMD1

    Clone
    Products:
         
    OriGene clones in human, mouse for AMD1 (see all 12)
    OriGene ORF clones in mouse, rat for AMD1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): AMD1 (NM_001634)
    Sino Biological Human cDNA Clone for AMD1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for AMD1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat AMD1

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for AMD1
    Browse ESI BIO Cell Lines and PureStem Progenitors for AMD1 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for AMD1


    (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
    cytosol4
    nucleus3
    extracellular1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol TAS--

    Find genes that share ontologies with AMD1           About GenesLikeMe


    (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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    SuperPaths for AMD1 About    
    See pathways by source

    SuperPathContained pathways About
    1Metabolism
    Metabolism0.38
    Metabolic pathways0.38
    2Metabolism of amino acids and derivatives
    Metabolism of amino acids and derivatives
    Metabolism of polyamines0.00
    3Sulfur amino acid metabolism
    Cysteine and methionine metabolism0.35
    4Arginine and proline metabolism
    Arginine and proline metabolism


    Find genes that share SuperPaths with AMD1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    1 Reactome Pathway for AMD1
        Metabolism of polyamines


    3 Kegg Pathways  (Kegg details for AMD1):
        Cysteine and methionine metabolism
    Arginine and proline metabolism
    Metabolic pathways

    UniProtKB/Swiss-Prot: DCAM_HUMAN, P17707
    Pathway: Amine and polyamine biosynthesis; S-adenosylmethioninamine biosynthesis; S-adenosylmethioninamine from
    S-adenosyl-L-methionine: step 1/1

        Pathway & Disease-focused RT2 Profiler PCR Arrays including AMD1: 

              cAMP / Ca2+ Signaling PathwayFinder in human mouse rat
              Amino Acid Metabolism I in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for AMD1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for AMD1 (P177073 ENSP000003578804) via UniProtKB, MINT, STRING, and/or I2D (see all 81)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H2BCP628073I2D: score=1 
    HIST1H2BEP628073I2D: score=1 
    HIST1H2BFP628073I2D: score=1 
    HIST1H2BGP628073I2D: score=1 
    HIST1H2BIP628073I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006557S-adenosylmethioninamine biosynthetic process IEA--
    GO:0006595polyamine metabolic process TAS--
    GO:0006597spermine biosynthetic process IEA--
    GO:0008295spermidine biosynthetic process IEA--
    GO:0034641cellular nitrogen compound metabolic process TAS--

    Find genes that share ontologies with AMD1           About GenesLikeMe



    (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 AMD1 (DCAM)

    10 HMDB Compounds for AMD1    About this table
    CompoundSynonyms CAS #PubMed Ids
    1,3-Diaminopropane1,3-Diamino-n-propane (see all 8)109-76-26798961
    Carbon dioxideCarbon oxide (see all 5)124-38-9--
    N1-AcetylspermineN'-Acetylspermine (see all 6)25593-72-0--
    NorspermidineN-(3-aminopropyl)-1,3-Propanediamine (see all 28)56-18-8--
    Putrescine1,4-Butanediamine (see all 8)110-60-1--
    Pyruvic acid2-Oxopropanoate (see all 14)127-17-3--
    S-Adenosylmethioninamine(5-deoxy-5-adenosyl)(3-aminopropyl) methylsulfonium salt (see all 7)22365-13-5--
    S-Adenosylmethionine(3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine (see all 16)29908-03-0--
    Spermidine1,5,10-Triazadecane (see all 15)124-20-9--
    Spermine1,5,10,14-Tetraazatetradecane (see all 18)71-44-3--

    4 DrugBank Compounds for AMD1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    S-AdenosylmethionineAcylcarnitine (see all 6)29908-03-0targetcofactor16515461 12974388 15051528 12545203
    Putrescine-- 110-60-1target--17139284 17016423
    Tris(Hydroxymethyl)Aminomethane-- --target--17139284 17016423
    5'-{[4-(aminooxy)butyl](methyl)amino}-5'-deoxy-8-ethenyladenosine-- --target--10592235

    Selected Novoseek inferred chemical compound relationships for AMD1 gene (see all 21)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sam 486a 96.4 14 9133651 (2), 8877009 (2), 10944598 (1), 16941339 (1) (see all 10)
    s-adenosylmethionine 95.2 156 11032186 (3), 9133651 (2), 12600205 (2), 7789170 (2) (see all 99)
    ethylglyoxal-bis-guanylhydrazone 92.9 12 7958401 (2), 1480164 (1), 9712522 (1), 8352568 (1)
    abeado 92.1 10 9133651 (2), 1637820 (1), 19419862 (1), 1301596 (1) (see all 5)
    methylglyoxal bis(guanylhydrazone) 91.7 29 1511437 (3), 1480164 (2), 8340919 (2), 8877009 (2) (see all 12)
    spermidine 91.4 61 9743591 (2), 1358085 (2), 8343127 (2), 15821146 (2) (see all 41)
    putrescine 90.8 51 9880821 (5), 12974388 (4), 16257247 (3), 9743591 (2) (see all 28)
    spermine 90.4 54 2344358 (4), 8395844 (2), 7945201 (2), 16515461 (2) (see all 38)
    ornithine 86.1 43 12686127 (2), 1511437 (2), 8205541 (2), 7656236 (1) (see all 37)
    dfmo 84.2 16 2114097 (3), 7634128 (1), 9743591 (1), 11698350 (1) (see all 11)



    Find genes that share compounds with AMD1           About GenesLikeMe



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for AMD1 gene (5 alternative transcripts): 
    NM_001287214.1  NM_001287216.1  NM_001634.5  NM_001033059.1  NM_001287215.1  

    Unigene Cluster for AMD1:

    Adenosylmethionine decarboxylase 1
    Hs.159118  [show with all ESTs]
    Unigene Representative Sequence: BX640599
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000368885(uc003puk.1 uc011eaz.1) ENST00000368882(uc003pul.1 uc011eba.1)
    ENST00000368876(uc011eay.1) ENST00000465404 ENST00000451850 ENST00000368877

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat AMD1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate AMD1 (see all 25):
    hsa-miR-21* hsa-miR-4288 hsa-miR-2110 hsa-miR-513a-5p hsa-miR-450a hsa-miR-632 hsa-miR-374a hsa-miR-132
    SwitchGear 3'UTR luciferase reporter plasmidAMD1 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for AMD1
    Predesigned siRNA for gene silencing in human, mouse, rat AMD1
    Clone
    Products:
         
    OriGene clones in human, mouse for AMD1 (see all 12)
    OriGene ORF clones in mouse, rat for AMD1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): AMD1 (NM_001634)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for AMD1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat AMD1
    Primer
    Products:
        
    OriGene qPCR primer pairs and template standards for AMD1
    OriGene qSTAR qPCR primer pairs in human, mouse for AMD1
    Pre-validated RT2 qPCR Primer Assay in human, mouse / rat AMD1
      QuantiTect SYBR Green Assays in human, mouse, rat AMD1
      QuantiFast Probe-based Assays in human, mouse, rat AMD1

    Additional mRNA sequence: 

    AJ420527.1 AJ420567.1 AK026205.1 AK130474.1 AK300330.1 AK302761.1 AK304351.1 AK316471.1 
    AL832698.1 BC000171.2 BX640599.1 M21154.1 

    Selected DOTS entries (see all 27):

    DT.95153293  DT.121356897  DT.100642958  DT.100824372  DT.456244  DT.100657843  DT.101984850  DT.100824365 
    DT.100824366  DT.95308707  DT.121356891  DT.100037909  DT.121356885  DT.121357065  DT.121357073  DT.100740399 
    DT.121357067  DT.121357095  DT.121357134  DT.91979581  DT.95153266  DT.95153275  DT.95153296  DT.95153299 

    Selected AceView cDNA sequences (see all 466):

    BF435395 AA327870 AA476644 BI858305 CR599478 BX108055 AW673681 AU120139 
    BU630354 AA769596 CA443041 AI091117 BX498600 AA960801 AW235553 CR610717 
    AK130474 CB112559 CA391228 AW150544 CA449342 R82299 CA308267 F03548 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for AMD1 (see all 7)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b · 9c ^ 10a · 10b
    SP1:                                                                                -                           
    SP2:                                                                                -                           
    SP3:              -                                                                                             
    SP4:                                                                                                            
    SP5:              -     -     -     -     -     -                                                               


    ECgene alternative splicing isoforms for AMD1

    (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)
    About This Section

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    AMD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTGTTGATTG
    AMD1 Expression
    About this image


    AMD1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 10) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Membranous Facial Bones
     
     Blood (Hematopoietic System)    fully expand to see all 2 entries
             Granulocytes Peripheral Blood
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 2 entries
             Mandibular Arch Muscles
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Cerebral Cortex
     
     Eye (Sensory Organs)
             Lens
    AMD1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    AMD1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.159118
        Pathway & Disease-focused RT2 Profiler PCR Arrays including AMD1: 
              cAMP / Ca2+ Signaling PathwayFinder in human mouse rat
              Amino Acid Metabolism I in human mouse rat

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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)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for AMD1 gene from Selected species (see all 24)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Amd11 , 5 S-adenosylmethionine decarboxylase 11, 5 95.91(n)1
    98.2(a)1
      10 (21.85 cM)5
    117021  NM_009665.51  NP_033795.11 
     402874585 
    chicken
    (Gallus gallus)
    Aves AMD11 adenosylmethionine decarboxylase 1 89.26(n)
    89.16(a)
      421755  NM_001012569.1  NP_001012587.1 
    lizard
    (Anolis carolinensis)
    Reptilia AMD16
    adenosylmethionine decarboxylase 1
    85(a)
    1 ↔ 1
    1(191999931-192020756)
    African clawed frog
    (Xenopus laevis)
    Amphibia amd1-prov2 S-Adenosylmethionine decarboxylase 1A 82.97(n)    BC042281.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc556142 similar to S-adenosylmethionine decarboxylase 1 78.79(n)   394055  BC045404.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta SamDC1 , 3 spermidine biosynthesis
    adenosylmethionine decarboxylase3
    S-adenosylmethionine decarboxylase1
    48(a)3
    56.25(n)1
    52.19(a)1
      31D93
    343961  NM_057875.51  NP_477223.21 
    worm
    (Caenorhabditis elegans)
    Secernentea smd-11 smd-1 49.54(n)
    43.34(a)
      173269  NM_061047.5  NP_493448.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SPE2(YOL052C)4
    SPE21
    S-adenosylmethionine decarboxylase, required for the more4
    SPE21
    46.28(n)1
    35.17(a)1
      15(233636-232446)4
    8541051, 4  NP_014590.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G159501 AT5G15950 50.06(n)
    41.57(a)
      831452  NM_001036811.1  NP_001031888.1 
    rice
    (Oryza sativa)
    Liliopsida Os09g04243001 Os09g0424300 48.28(n)
    41.91(a)
      4347103  NM_001069752.1  NP_001063217.1 


    ENSEMBL Gene Tree for AMD1 (if available)
    TreeFam Gene Tree for AMD1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for AMD1 gene
    1 SIMAP similar gene for AMD1 using alignment to 4 protein entries:     DCAM_HUMAN (see all proteins):
    DKFZp686G18136

    Find genes that share paralogs with AMD1           About GenesLikeMe


    Selected Pseudogenes.org Pseudogenes for AMD1 (see all 7)
    PGOHUM00000238685 PGOHUM00000234322 PGOHUM00000235215 PGOHUM00000243064 PGOHUM00000243286


    (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 AMD1 (see all 521)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs122055011,2
    C,F--111194307(+) ggtgcG/Cgtggc 2 -- us2k11Minor allele frequency- C:0.50NA 2
    rs26653591,2
    C,A,H--111194468(-) TGCCTC/TAGCCT 2 -- us2k17Minor allele frequency- T:0.08NA WA CSA 13
    rs1869813901,2
    --111194659(+) CGTTCC/TTGTAA 2 -- us2k10--------
    rs27967491,2
    C,F,A,H--111194703(+) AAACCG/CAAACC 2 -- us2k115Minor allele frequency- C:0.34NS EA NA WA CSA 791
    rs1171437261,2
    C,F--111194737(+) ATGTTG/AACATC 2 -- us2k11Minor allele frequency- A:0.03EA 120
    rs126638171,2
    C,H--111194777(+) TCTAAG/AGATGA 2 -- us2k15Minor allele frequency- A:0.00NS EA NA 422
    rs38405291,2
    C--111194934(-) TAAGT-/TAAGT 
            
    ATAAA
    2 -- us2k1 tfbs30--------
    rs9578241,2
    C,F,A,H--111195049(+) GAAGAT/CAGCAC 2 -- us2k113Minor allele frequency- C:0.12NS EA NA 1560
    rs747002271,2
    --111195174(+) GAAGTA/CGTTTT 2 -- us2k10--------
    rs1118713431,2
    C,F--111195297(+) GGGTAG/AAGCCG 2 -- us2k11Minor allele frequency- A:0.50NA 2

    HapMap Linkage Disequilibrium report for AMD1 (111195973 - 111216916 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for AMD1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv830773CNV Loss17160897
    nsv886538CNV Gain21882294
    nsv819336CNV Gain19587683

    Human Gene Mutation Database (HGMD): AMD1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing AMD1
    DNA2.0 Custom Variant and Variant Library Synthesis for AMD1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 180980    OMIM disorders: --

    3 diseases for AMD1:    
    About MalaCards
    chagas disease    sleeping sickness    malaria

    1 disease from the University of Copenhagen DISEASES database for AMD1:
    Sleeping sickness

    Find genes that share disorders with AMD1           About GenesLikeMe

    Selected Novoseek inferred disease relationships for AMD1 gene (see all 16)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    pneumocystis carinii infections 50 1 8340919 (1)
    bladder carcinoma 39.7 3 8340919 (1), 8421290 (1), 8205541 (1)
    melanoma b16 25.6 1 8205541 (1)
    colon cancer 18.4 7 11163334 (3), 9880821 (3)
    chagas disease 14.2 1 9677309 (1)
    cancer 8.54 7 17676832 (1), 11016654 (1), 15704548 (1), 10713131 (1) (see all 6)
    ischemia 0 2 1499693 (1)
    cancer lung 0 3 17558447 (1)
    breast cancer 0 4 8877009 (2), 7656236 (1), 15547724 (1)
    metastasis 0 2 11787064 (2)

    Genetic Association Database (GAD): AMD1
    Human Genome Epidemiology (HuGE) Navigator: AMD1 (4 documents)

    Export disorders for AMD1 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 AMD1 gene, integrated from 10 sources (see all 167):
    (articles sorted by number of sources associating them with AMD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The crystal structure of human S-adenosylmethionine decarboxylase at 2.25-A resolution reveals a novel fold. (PubMed id 10378277)1, 2, 9 Ekstrom J.L.... Ealick S.E. (Structure 1999)
    2. Mechanistic studies of the processing of human S-adenosylmethionine decarboxylase proenzyme. Isolation of an ester intermediate. (PubMed id 10574985)1, 2, 9 Xiong H. and Pegg A.E. (J. Biol. Chem. 1999)
    3. Amino acid residues necessary for putrescine stimulation of human S- adenosylmethionine decarboxylase proenzyme processing and catalytic activity. (PubMed id 1917972)1, 2, 9 Stanley B.A. and Pegg A.E. (J. Biol. Chem. 1991)
    4. A candidate gene study of folate-associated one carbon metabolism genes and colorectal cancer risk. (PubMed id 20615890)1, 4 Levine A.J....Haile R.W. (amp 2010)
    5. An association study of 45 folate-related genes in spina bifida: Involvement of cubilin (CUBN) and tRNA aspartic acid methyltransferase 1 (TRDMT1). (PubMed id 19161160)1, 4 Franke B....Blom H.J. (Birth Defects Res. Part A Clin. Mol. Teratol. 2009)
    6. Plasma complement components and activation fragments: associations with age-related macular degeneration genotypes and phenotypes. (PubMed id 19661236)1, 4 Reynolds R....Seddon J.M. (amp 2009)
    7. 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. (Genome Res. 2004)
    8. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
    9. The structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase. (PubMed id 11583147)1, 2 Tolbert W.D.... Ealick S.E. (Biochemistry 2001)
    10. Role of cysteine-82 in the catalytic mechanism of human S- adenosylmethionine decarboxylase. (PubMed id 10029540)1, 2 Xiong H.... Pegg A.E. (Biochemistry 1999)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 262 HGNC: 457 AceView: AMD1 Ensembl:ENSG00000123505 euGenes: HUgn262
    ECgene: AMD1 Kegg: 262 H-InvDB: AMD1

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for AMD1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for AMD1 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 AMD1 gene:
    Search GeneIP for patents involving AMD1

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



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