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

SMPDL3B Gene

protein-coding   GIFtS: 45
GCID: GC01P028261

sphingomyelin phosphodiesterase, acid-like 3B
 Explore 2 diseases affiliated with
SMPDL3B via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SMPDL3B    

Aliases
for SMPDL3B gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Sphingomyelin Phosphodiesterase, Acid-Like 3B1 2
ASML3B1 2 3
ASM-Like Phosphodiesterase 3b2 3
Acid Sphingomyelinase-Like Phosphodiesterase 3b2
EC 3.1.4.-3

External Ids:    HGNC: 214161   Entrez Gene: 272932   Ensembl: ENSG000001307687   UniProtKB: Q924853   

Export aliases for SMPDL3B gene to outside databases

Previous GC identifers: GC01P027867 GC01P027945 GC01P028134 GC01P026518


Summaries
for SMPDL3B gene

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

Genomic Views
for SMPDL3B gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_004610.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SMPDL3B gene promoter:
         SRF   C/EBPbeta   SRF (504 AA)   IRF-1   C/EBPalpha   CREB   PPAR-alpha   deltaCREB   c-Myb   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SMPDL3B promoter sequence
   Search SABiosciences Chromatin IP Primers for SMPDL3B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SMPDL3B


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

Entrez Gene cytogenetic band: 1p35.3   Ensembl cytogenetic band:  1p35.3   HGNC cytogenetic band: 1p35.3

SMPDL3B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMPDL3B gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P028261:  view genomic region     (about GC identifiers)

Start:
 28,261,504 bp from pter      End:
 28,285,668 bp from pter
Size:
 24,165 bases      Orientation:
 plus strand

Proteins
for SMPDL3B gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: ASM3B_HUMAN, Q92485 (See protein sequence)
Recommended Name: Acid sphingomyelinase-like phosphodiesterase 3b precursor  
Size: 455 amino acids; 50814 Da
Subcellular location: Secreted (By similarity)
Secondary accessions: B7ZB35 Q5T0Z0 Q96CB7
Alternative splicing: 2 isoforms:  Q92485-1   Q92485-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SMPDL3B: NX_Q92485

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q92485

    • SMPDL3B Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001009568.1  NP_055289.2  

    ENSEMBL proteins: 
     ENSP00000363001   ENSP00000449057   ENSP00000388092   ENSP00000362995   ENSP00000449450  
     ENSP00000403138  

    Human Recombinant Protein Products: 
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    Novus Biologicals SMPDL3B Proteins
    Novus Biologicals SMPDL3B Lysates
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for SMPDL3B

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space IEA--


    SMPDL3B for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for SMPDL3B

    Protein Domains /
    Families
    for SMPDL3B gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    SMPDL3B for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR004843 Metallo_PEstase_dom
     IPR017064 ASM-like_Pdiesterase_prd

    Graphical View of Domain Structure for InterPro Entry Q92485

    ProtoNet protein and cluster: Q92485

    UniProtKB/Swiss-Prot: ASM3B_HUMAN, Q92485
    Similarity: Belongs to the acid sphingomyelinase family


    Function
    for SMPDL3B gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Enzyme Number (IUBMB): EC 3.1.4.-1

    miRNA
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    Browse MicroRNA Expression Plasmids
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    2 QIAGEN miScript miRNA Assays for microRNAs that regulate SMPDL3B:
    hsa-miR-1207-5p hsa-miR-3150a-3p
    SwitchGear 3'UTR luciferase reporter plasmid: SMPDL3B 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SMPDL3B (see all 7)
    OriGene shRNA RFP: SMPDL3B
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    Gene Editing
    Products:    		DNA2.0 Custom Protein Engineering Service for SMPDL3B

    Clone
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    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SMPDL3B (see all 4)
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    Cell Line
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    Search LifeMap BioReagents cell lines for SMPDL3B

    In Situ Assay
    Products:       
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004767sphingomyelin phosphodiesterase activity IEA--
    GO:0016787hydrolase activity ----
    GO:0016798hydrolase activity, acting on glycosyl bonds IEA--


    SMPDL3B for ontologies           About GeneDecksing


    Animal Models:
         2 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Smpdl3b):
     behavior/neurological  other 

    SMPDL3B for phenotypes           About GeneDecksing


    Pathways & Interactions
    for SMPDL3B gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SMPDL3B

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006685sphingomyelin catabolic process IEA--


    SMPDL3B for ontologies           About GeneDecksing



    Drugs & Compounds
    for SMPDL3B gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SMPDL3B
    Search CenterWatch for drugs/clinical trials and news about SMPDL3B / ASM3B 

    Transcripts
    for SMPDL3B gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for SMPDL3B gene (2 alternative transcripts): 
    NM_001009568.1  NM_014474.2  

    Unigene Cluster for SMPDL3B:

    Sphingomyelin phosphodiesterase, acid-like 3B
    Hs.123659  [show with all ESTs]
    Unigene Representative Sequence: AK293566
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000373894(uc001bpg.3 uc010ofr.2) ENST00000548116(uc010ofq.2)
    ENST00000411604 ENST00000373888(uc001bpf.3) ENST00000466793 ENST00000549094
    ENST00000412515

    miRNA
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    2 QIAGEN miScript miRNA Assays for microRNAs that regulate SMPDL3B:
    hsa-miR-1207-5p hsa-miR-3150a-3p
    SwitchGear 3'UTR luciferase reporter plasmid: SMPDL3B 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SMPDL3B (see all 7)
    OriGene shRNA RFP: SMPDL3B
    OriGene siRNA: SMPDL3B
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SMPDL3B
    Clone
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    Primer
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    Additional cDNA sequence: 

    AK293489.1 AK293566.1 AK301349.1 AK316500.1 BC014444.1 Y08134.1 

    4 DOTS entries:

    DT.209935  DT.100775446  DT.102823217  DT.121445257 

    24/69 AceView cDNA sequences (see all 69):

    BE271909 AA635056 AU076428 BM795371 AU099361 AU105491 AA928880 AU105486 
    CR613549 CA489839 CB160850 BQ710341 BM924641 BM977946 BI793138 CA438608 
    BU541750 BE999992 BM048081 BP352405 AL569955 CA425405 AW015709 CF144505 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for SMPDL3B (see all 7)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12a · 12b ^ 13
    SP1:                                -     -     -     -                 -                                                               
    SP2:                                                                                                                          -         
    SP3:                                -     -     -                       -                                                               
    SP4:                                -                                                                                                   
    SP5:                                -     -     -     -           -     -     -                                                         


    ECgene alternative splicing isoforms for SMPDL3B

    Expression
    for SMPDL3B gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SMPDL3B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CGTTTGAAAA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    SMPDL3B expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    TestisSeminiferous TubulesSertoli cellsTestis
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 2 LifeMap Cells 
    NameCategory
    ES04(HES-4) (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    Line H9 (WA09) (Embryonic Stem Cell)Early Embryo, Inner Cell Mass

    See SMPDL3B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SMPDL3B

    SOURCE GeneReport for Unigene cluster: Hs.123659
        SABiosciences Custom PCR Arrays for SMPDL3B
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    In Situ
    Assay Products:     
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    Orthologs
    for SMPDL3B gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for SMPDL3B gene from 5/24 species (see all 24)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves SMPDL3B1 sphingomyelin phosphodiesterase, acid-like 3B 64.57(n)
    62.11(a)    		   769013  NM_001252280.1  NP_001239209.1 
    lizard
    (Anolis carolinensis)    		 Reptilia SMPDL3B6
    		 --
    		 59(a)
    		 1 ↔ 1
    		 GL343743.1(63482-70782)
    zebrafish
    (Danio rerio)    		 Actinopterygii LOC5643921 acid sphingomyelinase-like phosphodiesterase 3b-like 61.6(n)
    55.99(a)    		   564392  XM_687730.5  XP_692822.2 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG320521 CG32052 51.57(n)
    40.19(a)    		   326184  NM_168375.3  NP_729555.3 
    worm
    (Caenorhabditis elegans)    		 Secernentea ZK856.51 Protein ZK856.5 46.86(n)
    37.74(a)    		   191439  NM_073219.4  NP_505620.3 


    ENSEMBL Gene Tree for SMPDL3B (if available)
    TreeFam Gene Tree for SMPDL3B (if available) 

    Paralogs
    for SMPDL3B gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SMPDL3B gene
    SMPDL3A2  SMPD12  
    1 SIMAP similar gene for SMPDL3B using alignment to 5 protein entries:     ASM3B_HUMAN (see all proteins):
    SMPDL3A

    SMPDL3B for paralogs           About GeneDecksing



    Genomic Variants
    for SMPDL3B gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/12 NCBI SNPs in SMPDL3B are shown (see all 12)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 1 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs350450171,2
    		C--28260464(+) TTTTT-/TGAGAC 2 -- us2k11Minor allele frequency- T:0.00NA 2
    rs722661871,2
    		C--28266326(+) TTGTT-/TTTG  
                TTTGT     		1 -- int10--------
    rs1416706451,2
    		C,--28266326(+) TTGTT-/TTTG  
                TTTGT     		2 -- int10--------
    rs562347191,2
    		C--28266329(+) TGTTT-/GTTT  
                TTGTA     		1 -- int11Minor allele frequency- GTTT:0.00NA 2
    rs560435531,2
    		C,--28266956(+) TATGACGTTC   
      TGTT    /-    AATCA     		2 -- int11Minor allele frequency- -:0.50CSA 2
    rs113860581,2
    		C,--28268833(+) TCCCCG/-CAACA 2 -- int11Minor allele frequency- -:0.00NA 2
    rs57732061,2
    		C--28270524(+) aaaaa-/AgaaaC 1 -- int1 trp31Minor allele frequency- A:0.00NA 2
    rs715868181,2
    		C,F--28278678(+) AGGGAT/-TTTTT 2 -- int12Minor allele frequency- -:0.50NA CSA 4
    rs345508721,2
    		----28259504(+) CAGGG-/GAAACT 2 -- us2k10--------
    rs1133544211,2
    		----28274170(+) TTTTTG/-TTTTT 2 -- int11Minor allele frequency- -:0.00CSA 2

    HapMap Linkage Disequilibrium report for SMPDL3B (28261504 - 28285668 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for SMPDL3B: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SMPDL3B
    DNA2.0 Custom Variant and Variant Library Synthesis for SMPDL3B

    Disorders / Diseases
    for SMPDL3B gene

    (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.)
    About This Section
    SMPDL3B for disorders           About GeneDecksing

    2 diseases for SMPDL3B:    About MalaCards
    intrahepatic cholangiocarcinoma    cholangiocarcinoma


    Export disorders for SMPDL3B gene to outside databases

    Publications
    for SMPDL3B gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SMPDL3B gene integrated from 9 sources:
    (articles sorted by number of sources associating them with SMPDL3B)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    2. 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. (2004)
    3. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (PubMed id 16712791)1 Wang A.G....Kim N.S. (2006)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    6. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)
    7. Generation of biologically active linear and cyclic peptides has revealed a unique fine specificity of rituximab and its possible cross-reactivity with acid sphingomyelinase-like phosphodiesterase 3b precursor. (PubMed id 16223774)9 Perosa F....Dammacco F. (2006)

    External Searches for SMPDL3B gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing SMPDL3B gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 27293 HGNC: 21416 AceView: SMPDL3B Ensembl:ENSG00000130768 euGenes: HUgn27293
    ECgene: SMPDL3B H-InvDB: SMPDL3B

    Other Databases showing SMPDL3B gene

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    Specialized Databases showing SMPDL3B gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SMPDL3B Pharmacogenomics, SNPs, Pathways

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    		Patent Information for SMPDL3B gene:
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