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SGMS2 Gene

protein-coding   GIFtS: 57
GCID: GC04P108745

Sphingomyelin Synthase 2

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(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Sphingomyelin Synthase 21 2 3
SMS22 3 5
EC 2.7.8.273 8
Phosphatidylcholine:Ceramide Cholinephosphotransferase 22
SM Synthase2

External Ids:    HGNC: 283951   Entrez Gene: 1669292   Ensembl: ENSG000001640237   OMIM: 6115745   UniProtKB: Q8NHU33   
ORGUL members:         

Export aliases for SGMS2 gene to outside databases

Previous GC identifers: GC04P108966 GC04P104477


(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 SGMS2 Gene:
Sphingomyelin, a major component of cell and Golgi membranes, is made by the transfer of phosphocholine from
phosphatidylcholine onto ceramide, with diacylglycerol as a side product. The protein encoded by this gene is an
enzyme that catalyzes this reaction primarily at the cell membrane. The synthesis is reversible, and this enzyme
can catalyze the reaction in either direction. The encoded protein is required for cell growth. Three transcript
variants encoding the same protein have been found for this gene. There is evidence for more variants, but the
full-length nature of their transcripts has not been determined.(provided by RefSeq, Oct 2008)

GeneCards Summary for SGMS2 Gene:
SGMS2 (sphingomyelin synthase 2) is a protein-coding gene. GO annotations related to this gene include ceramide cholinephosphotransferase activity and kinase activity. An important paralog of this gene is SAMD8.

UniProtKB/Swiss-Prot: SMS2_HUMAN, Q8NHU3
Function: Sphingomyelin synthases synthesize the sphingolipid, sphingomyelin, through transfer of the phosphatidyl
head group, phosphatidylcholine, on to the primary hydroxyl of ceramide. The reaction is bidirectional depending
on the respective levels of the sphingolipid and ceramide. Plasma membrane SMS2 can also convert
phosphatidylethanolamine (PE) to ceramide phosphatidylethanolamine (CPE). Major form in liver. Required for cell
growth in certain cell types. Regulator of cell surface levels of ceramide, an important mediator of signal
transduction and apoptosis. Regulation of sphingomyelin (SM) levels at the cell surface affects insulin
sensitivity




(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_000004.11  NT_016354.20  NC_018915.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SGMS2 gene promoter:
         TBP   COUP-TF1   C/EBPbeta   COUP   HNF-4alpha2   GATA-1   HNF-4alpha1   COUP-TF   Cart-1   LyF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSGMS2 promoter sequence
   Search Chromatin IP Primers for SGMS2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SGMS2


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

Entrez Gene cytogenetic band: 4q25   Ensembl cytogenetic band:  4q25   HGNC cytogenetic band: 4q25

SGMS2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SGMS2 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P108745:  view genomic region     (about GC identifiers)

Start:
108,745,719 bp from pter      End:
108,836,203 bp from pter
Size:
90,485 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SMS2_HUMAN, Q8NHU3 (See protein sequence)
Recommended Name: Phosphatidylcholine:ceramide cholinephosphotransferase 2  
Size: 365 amino acids; 42280 Da
Miscellaneous: Overexpression of the human protein in mouse causes increased non-HDL-sphingomyelin and non-HDL
cholesterol levels, decreased HDL-sphingomyelin and HDL-cholesterol levels and increases lipoprotein atherogenic
potential
Secondary accessions: A8K2S9 B2RA61

Explore the universe of human proteins at neXtProt for SGMS2: NX_Q8NHU3

Explore proteomics data for SGMS2 at MOPED

Post-translational modifications: 

  • Palmitoylated on Cys-331, Cys-332, Cys-343 and Cys-348; which plays an important role in plasma membrane
    localization1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for SGMS2 (Q8NHU3) (see all 5)
     GGGLSITGSH  VVHERVPPKE  AYYITTRLFWWYH  LTLTYLFIKEYSPR 


    See SGMS2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001129729.1  NP_001129730.1  NP_689834.1  

    ENSEMBL proteins: 
     ENSP00000378176   ENSP00000428176   ENSP00000351981   ENSP00000428294   ENSP00000378178  
     ENSP00000430172  
    Reactome Protein details: Q8NHU3

    SGMS2 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for SGMS2

     
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    antibodies-online proteins for SGMS2 (3 products) 

     
    antibodies-online peptides for SGMS2

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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:
     IPR025749 Sphingomyelin_synth-like_dom

    Graphical View of Domain Structure for InterPro Entry Q8NHU3

    ProtoNet protein and cluster: Q8NHU3

    UniProtKB/Swiss-Prot: SMS2_HUMAN, Q8NHU3
    Similarity: Belongs to the sphingomyelin synthase family


    Find genes that share domains with SGMS2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: SMS2_HUMAN, Q8NHU3
    Function: Sphingomyelin synthases synthesize the sphingolipid, sphingomyelin, through transfer of the phosphatidyl
    head group, phosphatidylcholine, on to the primary hydroxyl of ceramide. The reaction is bidirectional depending
    on the respective levels of the sphingolipid and ceramide. Plasma membrane SMS2 can also convert
    phosphatidylethanolamine (PE) to ceramide phosphatidylethanolamine (CPE). Major form in liver. Required for cell
    growth in certain cell types. Regulator of cell surface levels of ceramide, an important mediator of signal
    transduction and apoptosis. Regulation of sphingomyelin (SM) levels at the cell surface affects insulin
    sensitivity
    Catalytic activity: A ceramide + a phosphatidylcholine = a sphingomyelin + a 1,2-diacyl-sn-glycerol
    Enzyme regulation: Inhibited by bacterial PC-phospholipase C inhibitor D609

         Enzyme Number (IUBMB): EC 2.7.8.271 2

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:0016301kinase activity IEA--
    GO:0033188sphingomyelin synthase activity IEA--
    GO:0047493ceramide cholinephosphotransferase activity IDA14685263
         
    Find genes that share ontologies with SGMS2           About GenesLikeMe


    Phenotypes:
         7 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Sgms2):
     adipose tissue  cellular  growth/size/body  hematopoietic system  homeostasis/metabolism 
     immune system  liver/biliary system 

    Find genes that share phenotypes with SGMS2           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Sgms2tm1Jia for SGMS2

       genOway: Develop your customized and physiologically relevant rodent model for SGMS2

    miRNA
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    miRTarBase miRNAs that target SGMS2:
    hsa-mir-192-5p (MIRT026582), hsa-mir-615-3p (MIRT040261), hsa-mir-375 (MIRT019865)

    Block miRNA regulation of human, mouse, rat SGMS2 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SGMS2 (see all 79):
    hsa-miR-579 hsa-miR-4305 hsa-miR-30d hsa-miR-219-5p hsa-miR-342-3p hsa-miR-30a hsa-miR-409-5p hsa-miR-3622a-5p
    SwitchGear 3'UTR luciferase reporter plasmidSGMS2 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SGMS2


    (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 UniProtKB/Swiss-Prot
    SMS2_HUMAN, Q8NHU3: Cell membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane
    protein. Note=Predominantly plasma membrane, some in Golgi apparatus. Some localization in the perinuclear region
    where it colocalizes with a sialyltransferase
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    golgi apparatus5
    plasma membrane5
    peroxisome2
    cytosol1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005794Golgi apparatus IDA14685263
    GO:0005886plasma membrane TAS--
    GO:0005887integral component of plasma membrane IDA14685263
    GO:0016020membrane ----
    GO:0030173integral component of Golgi membrane IDA14685263

    Find genes that share ontologies with SGMS2           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 SGMS2 About    
    See pathways by source

    SuperPathContained pathways About
    1Sphingolipid metabolism
    Sphingolipid metabolism0.61
    Sphingolipid de novo biosynthesis0.46
    Sphingolipid metabolism0.61
    Sphingolipid Metabolism0.42
    2Metabolism
    Metabolism0.38
    Metabolism of lipids and lipoproteins0.37
    Metabolic pathways0.38
    3sphingomyelin metabolism/ceramide salvage
    sphingomyelin metabolism/ceramide salvage


    Find genes that share SuperPaths with SGMS2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2 BioSystems Pathways for SGMS2
        Sphingolipid Metabolism
    sphingomyelin metabolism/ceramide salvage


    1 Reactome Pathway for SGMS2
        Sphingolipid de novo biosynthesis


    2 Kegg Pathways  (Kegg details for SGMS2):
        Sphingolipid metabolism
    Metabolic pathways

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SGMS2
    Interactions:

        Search GeneGlobe Interaction Network for SGMS2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 22)

    Selected Interacting proteins for SGMS2 (ENSP000003519814) via UniProtKB, MINT, STRING, and/or I2D (see all 22)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ACER1ENSP000003014524STRING: ENSP00000301452
    ASAH1ENSP000003711524STRING: ENSP00000371152
    ASAH2ENSP000003788974STRING: ENSP00000378897
    CERKENSP000002162644STRING: ENSP00000216264
    DEGS1ENSP000003164764STRING: ENSP00000316476
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006665sphingolipid metabolic process TAS--
    GO:0006686sphingomyelin biosynthetic process IDA14685263
    GO:0030148sphingolipid biosynthetic process TAS--
    GO:0044281small molecule metabolic process TAS--

    Find genes that share ontologies with SGMS2           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 SGMS2 (SMS2)

    Selected HMDB Compounds for SGMS2 (see all 2027)    About this table
    CompoundSynonyms CAS #PubMed Ids
    PC(O-16:0/18:2(9Z,12Z))1-hexadecyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine (see all 5)88542-95-412486725
    Cer(d18:0/12:0) ----
    Cer(d18:0/14:0) ----
    Cer(d18:0/16:0) ----
    Cer(d18:0/18:0) ----
    Cer(d18:0/18:1(11Z)) ----
    Cer(d18:0/18:1(9Z)) ----
    Cer(d18:0/20:0) ----
    Cer(d18:0/22:0) ----
    Cer(d18:0/22:1(13Z)) ----



    (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 SGMS2 gene (3 alternative transcripts): 
    NM_001136257.1  NM_001136258.1  NM_152621.5  

    Unigene Cluster for SGMS2:

    Sphingomyelin synthase 2
    Hs.595423  [show with all ESTs]
    Unigene Representative Sequence: NM_152621
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000506462 ENST00000394684(uc003hyl.4 uc003hyn.3 uc003hyo.3)
    ENST00000515332 ENST00000503862 ENST00000359079 ENST00000506993 ENST00000394686
    ENST00000503385 ENST00000504754
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SGMS2 (see all 79):
    hsa-miR-579 hsa-miR-4305 hsa-miR-30d hsa-miR-219-5p hsa-miR-342-3p hsa-miR-30a hsa-miR-409-5p hsa-miR-3622a-5p
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    Additional mRNA sequence: 

    AF452717.1 AK290344.1 AK314049.1 AL833599.1 BC028705.1 BC041369.2 BX649142.1 

    4 DOTS entries:

    DT.99940162  DT.95297202  DT.97805078  DT.121276427 

    Selected AceView cDNA sequences (see all 95):

    AA044286 CA405597 BU680203 BP350971 AI453293 CB104727 AA633946 CD244288 
    AF452717 BC028705 BM129814 AI888498 AL833599 H01973 BI492198 BX499403 
    CD366204 AL703028 BX649142 BM129624 AI139339 BM992772 BU680973 BC041369 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SGMS2 (see all 8)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c · 4d ^ 5 ^ 6a · 6b · 6c · 6d · 6e · 6f ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
    SP1:                                                  -     -     -                                                     -     -               
    SP2:                                                              -                                                     -     -               
    SP3:                                -     -     -     -     -     -                                                                           
    SP4:                    -                 -     -     -     -     -                                                                           
    SP5:                    -           -     -     -     -     -     -                                                                           


    ECgene alternative splicing isoforms for SGMS2

    (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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    SGMS2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTTGTGATTT
    SGMS2 Expression
    About this image


    SGMS2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 12) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 7 entries
             Membranous Facial Bones
     
     Brain (Nervous System)    fully expand to see all 5 entries
             Adult Endothelial Cells Blood Brain Barrier
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
             Line H9 (Naive)
     
     Testis (Reproductive System)    fully expand to see all 2 entries
             Sertoli cells Seminiferous Tubules
    SGMS2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SGMS2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.595423

    UniProtKB/Swiss-Prot: SMS2_HUMAN, Q8NHU3
    Tissue specificity: Brain, heart, kidney, liver, muscle and stomach. Also expressed in a number of cell lines such
    as carcinoma HeLa cells, hepatoma Hep-G2 cells, and colon carcinoma Caco-2 cells

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SGMS2

    (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 SGMS2 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sgms21 , 5 sphingomyelin synthase 21, 5 85.66(n)1
    91.51(a)1
      3 (60.91 cM)5
    744421  NM_028943.51  NP_083219.21 
     1313189855 
    chicken
    (Gallus gallus)
    Aves SGMS21 sphingomyelin synthase 2 80.55(n)
    89.04(a)
      422529  NM_001277826.1  NP_001264755.1 
    lizard
    (Anolis carolinensis)
    Reptilia SGMS26
    sphingomyelin synthase 2
    87(a)
    1 ↔ 1
    GL343384.1(366290-397823)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia sgms21 sphingomyelin synthase 2 73.79(n)
    78.08(a)
      496853  NM_001011385.2  NP_001011385.2 
    zebrafish
    (Danio rerio)
    Actinopterygii sgms21 sphingomyelin synthase 2 62.93(n)
    63.22(a)
      556193  NM_001145563.1  NP_001139035.1 
    worm
    (Caenorhabditis elegans)
    Secernentea sms-26
    sms-16
    (see all 3)
    Protein SMS-1, isoform b
    (see all 3)
    27(a)
    24(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    X(944939-948885) WBGene00004893
    IV(11482669-11498167) WBGene00004892


    ENSEMBL Gene Tree for SGMS2 (if available)
    TreeFam Gene Tree for SGMS2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SGMS2 gene
    SAMD82  SGMS12  
    3 SIMAP similar genes for SGMS2 using alignment to 4 protein entries:     SMS2_HUMAN (see all proteins):
    TMEM23    SGMS1    SAMD8

    Find genes that share paralogs with SGMS2           About GenesLikeMe



    (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 SGMS2 (see all 1572)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1878095631,2
    --108743788(+) CAGGCA/GACAGA 1 -- us2k10--------
    rs18451781,2
    C,F,A,H--108743816(+) AAAAAT/ATTTTT 1 -- us2k18Minor allele frequency- A:0.19NA WA CSA EA 367
    rs762455541,2
    C--108743880(+) ATTTTG/TATATA 1 -- us2k10--------
    rs1924324391,2
    --108743913(+) CATCAA/GAGTAA 1 -- us2k10--------
    rs1150207611,2
    F--108744114(+) CAGCCT/CCTGGT 1 -- us2k11Minor allele frequency- C:0.03NA 120
    rs1390699191,2
    --108744306(+) CTCCAC/TGGGTA 1 -- us2k10--------
    rs1429653861,2
    --108744536(+) TTATAC/GTTTTT 1 -- us2k10--------
    rs99966171,2
    C,F--108744575(+) TTTTTT/CCCACA 1 -- us2k1 trp33Minor allele frequency- C:0.07WA NA EA 358
    rs1135254051,2
    F--108744585(+) AACCTC/AGCCAG 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs2009929231,2
    --108744698(+) TTAGA-/TTTTTT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SGMS2 (108745719 - 108836203 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for SGMS2:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2677080CNV Deletion23128226
    nsv4457CNV Insertion18451855
    nsv461611CNV Loss19166990
    dgv5673n71CNV Loss21882294
    esv21916CNV Loss19812545
    nsv830031CNV Gain17160897

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SGMS2
    DNA2.0 Custom Variant and Variant Library Synthesis for SGMS2

    (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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    OMIM gene information: 611574    OMIM disorders: --


    Find genes that share disorders with SGMS2           About GenesLikeMe

    Genetic Association Database (GAD): SGMS2
    Human Genome Epidemiology (HuGE) Navigator: SGMS2 (1 document)

    Export disorders for SGMS2 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 SGMS2 gene, integrated from 10 sources (see all 27):
    (articles sorted by number of sources associating them with SGMS2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of a family of animal sphingomyelin synthases. (PubMed id 14685263)1, 2, 3 Huitema K.... Holthuis J.C. (EMBO J. 2004)
    2. Sphingomyelin synthase 2 is palmitoylated at the COOH-terminal tail, which is involved in its localization in plasma membranes. (PubMed id 19233134)1, 2, 9 Tani M. and Kuge O. (Biochem. Biophys. Res. Commun. 2009)
    3. A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. (PubMed id 20332099)1, 4 Kalsi G....Riley B.P. (Hum. Mol. Genet. 2010)
    4. The domain responsible for sphingomyelin synthase (SMS) activity. (PubMed id 18694848)1, 2 Yeang C.... Jiang X.C. (Biochim. Biophys. Acta 2008)
    5. Both sphingomyelin synthases SMS1 and SMS2 are required for sphingomyelin homeostasis and growth in human HeLa cells. (PubMed id 17449912)1, 2 Tafesse F.G.... Holthuis J.C.M. (J. Biol. Chem. 2007)
    6. 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)
    7. 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)
    8. Adenovirus-mediated sphingomyelin synthase 2 increases atherosclerotic lesions in ApoE KO mice. (PubMed id 21235823)1 Wang X....Wu M. (Lipids Health Dis 2011)
    9. Sphingomyelin and sphingomyelin synthase (SMS) in the malignant transformation of glioma cells and in 2-hydroxyoleic acid therapy. (PubMed id 22106271)1 BarcelA^-Coblijn G....EscribA! P.V. (Proc. Natl. Acad. Sci. U.S.A. 2011)
    10. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)

    (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: 166929 HGNC: 28395 AceView: MGC26963 Ensembl:ENSG00000164023 euGenes: HUgn166929
    ECgene: SGMS2 Kegg: 166929 H-InvDB: SGMS2

    (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 SGMS2 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 SGMS2 gene:
    Search GeneIP for patents involving SGMS2

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



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