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SAMD5 Gene

protein-coding   GIFtS: 39
GCID: GC06P147873

Sterile Alpha Motif Domain Containing 5

  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
Sterile Alpha Motif Domain Containing 51 2
SAM Domain-Containing Protein 52 3
dJ875H10.12
SAM Domain Containing 12
Sterile Alpha Motif Domain-Containing Protein 52
SAMDC13

External Ids:    HGNC: 211801   Entrez Gene: 3894322   Ensembl: ENSG000002037277   UniProtKB: Q5TGI43   

Export aliases for SAMD5 gene to outside databases

Previous GC identifers: GC00U914193 GC06U900641 GC06P145393


(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 SAMD5 Gene:
SAMD5 (sterile alpha motif domain containing 5) is a protein-coding gene. Diseases associated with SAMD5 include obesity, and hiv-1.


(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:
NC_000006.12  NC_018917.2  NT_025741.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the SAMD5 gene promoter:
         Olf-1   STAT5A   NF-E2 p45   AREB6   POU2F1   POU2F1a   Pax-4a   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSAMD5 promoter sequence
   Search Chromatin IP Primers for SAMD5

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SAMD5


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

Entrez Gene cytogenetic band: 6q24.3   Ensembl cytogenetic band:  6q24.3   HGNC cytogenetic band: 6q24.3

SAMD5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SAMD5 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P147873:  view genomic region     (about GC identifiers)

Start:
147,829,828 bp from pter      End:
148,058,683 bp from pter
Size:
228,856 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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SAMD5_HUMAN, Q5TGI4 (See protein sequence)
Recommended Name: Sterile alpha motif domain-containing protein 5  
Size: 173 amino acids; 19231 Da

Explore the universe of human proteins at neXtProt for SAMD5: NX_Q5TGI4

Explore proteomics data for SAMD5 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SAMD5 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001025231.1  
    ENSEMBL proteins: 
     ENSP00000356444   ENSP00000456528  

    SAMD5 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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    HGNC Gene Families:
    SAMD: Sterile alpha motif (SAM) domain containing

    3 InterPro protein domains:
     IPR021129 SAM_type1
     IPR013761 SAM/pointed
     IPR001660 SAM

    Graphical View of Domain Structure for InterPro Entry Q5TGI4

    ProtoNet protein and cluster: Q5TGI4

    1 Blocks protein domain: IPB001660 Sterile alpha motif SAM

    UniProtKB/Swiss-Prot: SAMD5_HUMAN, Q5TGI4
    Similarity: Contains 1 SAM (sterile alpha motif) domain


    SAMD5 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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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    SAMD5 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SAMD5
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    hsa-mir-21-5p (MIRT030748)

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    Selected qRT-PCR Assays for microRNAs that regulate SAMD5 (see all 47):
    hsa-miR-3130-5p hsa-miR-607 hsa-miR-938 hsa-miR-488 hsa-miR-371-5p hsa-miR-29b-1* hsa-miR-3613-3p hsa-miR-376c
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SAMD5


    (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
    extracellular1

    (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 SAMD5
    Interactions:

        Search GeneGlobe Interaction Network for SAMD5

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for SAMD5 (ENSP000003564444) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPOXENSP000003439434STRING: ENSP00000343943
    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 SAMD5



    (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,
    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 SAMD5 gene: 
    NM_001030060.2  

    Unigene Cluster for SAMD5:

    Sterile alpha motif domain containing 5
    Hs.567973  [show with all ESTs]
    Unigene Representative Sequence: NM_001030060
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000367474(uc003qmc.2) ENST00000566741
    miRNA
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    hsa-miR-3130-5p hsa-miR-607 hsa-miR-938 hsa-miR-488 hsa-miR-371-5p hsa-miR-29b-1* hsa-miR-3613-3p hsa-miR-376c
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector: SAMD5 (NM_001030060)
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    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat SAMD5
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SAMD5
      QuantiTect SYBR Green Assays in human, mouse, rat SAMD5
      QuantiFast Probe-based Assays in human, mouse, rat SAMD5

    Additional mRNA sequence: BC020896.1 

    2 DOTS entries:

    DT.91741375  DT.407224 

    Selected AceView cDNA sequences (see all 70):

    BX099879 BF115069 CA843432 BM717307 AA252168 BX110596 AA582100 AA452295 
    BM311407 AW274555 AA242983 BU102088 CA942632 BX099467 AA886794 AI221792 
    BX957080 AI700341 BX487881 BG566022 BG204892 BC020896 CD674346 BU739124 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, 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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    SAMD5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CACACTGTGA
    SAMD5 Expression
    About this image


    SAMD5 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Heart (Cardiovascular System)
             Endocardial Tube Cells Endocardium
    SAMD5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SAMD5 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.567973
        Custom PCR Arrays for SAMD5
    Primer
    Products:
    OriGene qSTAR qPCR primer pairs in human, mouse for SAMD5
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SAMD5
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    QuantiFast Probe-based Assays in human, mouse, rat SAMD5
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SAMD5

    (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 SAMD5 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Samd51 , 5 sterile alpha motif domain containing 51, 5 87.6(n)1
    90.7(a)1
      10 (3.15 cM)5
    3208251  NM_177271.31  NP_796245.21 
     96272595 
    chicken
    (Gallus gallus)
    Aves SAMD56
    sterile alpha motif domain containing 5
    89(a)
    1 ↔ 1
    3(46522593-46647011)
    lizard
    (Anolis carolinensis)
    Reptilia SAMD56
    sterile alpha motif domain containing 5
    62(a)
    1 ↔ 1
    1(208075115-208084161)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1001485611 sterile alpha motif domain-containing protein 5-like 59.23(n)
    62.16(a)
      100148561  XM_005158601.1  XP_005158658.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta SKIP6
    CG343776
    --
    7(a)
    16(a)
    many → 1
    many → 1
    3R(17959557-18121848)
    3R(18135203-18149816)


    ENSEMBL Gene Tree for SAMD5 (if available)
    TreeFam Gene Tree for SAMD5 (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 SAMD5 (see all 1303)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs715664781,2
    C--147827880(+) TGAGTT/CTGGGG 1 -- us2k13Minor allele frequency- C:0.05NA EA 242
    rs1166544871,2
    F--147828054(+) AACTCG/AGTTCC 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs735785711,2
    C,F--147828056(+) CTCGGT/CTCCGG 1 -- us2k12Minor allele frequency- C:0.11WA 120
    rs1851992121,2
    --147828120(+) TCCGCA/GTTGGT 1 -- us2k10--------
    rs359872081,2
    C,F--147828144(+) CTAAGC/GAGACA 1 -- us2k13Minor allele frequency- G:0.06NA EA 242
    rs773918201,2
    C--147828242(+) TTGGGT/GGCGCC 1 -- us2k12Minor allele frequency- G:0.08CSA WA 120
    rs1122793161,2
    F--147828557(+) GTACCT/AGCCCC 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs775243861,2
    F--147828692(+) TGATGG/CGGAAA 1 -- us2k11Minor allele frequency- C:0.03WA 118
    rs1830749081,2
    --147829320(+) GCGCCG/TTGGGG 1 -- us2k10--------
    rs1169804591,2
    C,F--147829670(+) CGGGCG/TGCACT 1 -- us2k11Minor allele frequency- T:0.23EA 120

    HapMap Linkage Disequilibrium report for SAMD5 (147829828 - 148058683 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for SAMD5:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2662219CNV Deletion23128226
    nsv819870CNV Gain19587683

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SAMD5
    DNA2.0 Custom Variant and Variant Library Synthesis for SAMD5

    (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.)
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    4 diseases for SAMD5:    
    About MalaCards
    obesity    hiv-1    alzheimer's disease    malaria


    SAMD5 for disorders           About GeneDecksing

    Genetic Association Database (GAD): SAMD5

    Export disorders for SAMD5 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 SAMD5 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SAMD5)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Common genetic variation and the control of HIV-1 in humans. (PubMed id 20041166)1, 4 Fellay J....Goldstein D.B. (PLoS Genet. 2009)
    2. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)
    3. Genome-wide scan of copy number variation in late-onset Alzheimer's disease. (PubMed id 20061627)4 Heinzen E.L....Goldstein D.B. (J. Alzheimers Dis. 2010)
    4. Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project. (PubMed id 17903300)4 Fox C.S....Atwood L.D. (BMC Med. Genet. 2007)
    5. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)2 Mungall A.J.... Beck S. (Nature 2003)
    6. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 389432 HGNC: 21180 AceView: LOC389432 Ensembl:ENSG00000203727 euGenes: HUgn389432
    ECgene: SAMD5 H-InvDB: SAMD5

    (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 SAMD5 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SAMD5 gene:
    Search GeneIP for patents involving SAMD5

    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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    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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