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

SBDS Gene

protein-coding   GIFtS: 66
GCID: GC07M066452

Shwachman-Bodian-Diamond Syndrome

  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)
About This Section

Aliases
Shwachman-Bodian-Diamond Syndrome1 2
SDS2 5
SWDS2
Ribosome Maturation Protein SBDS2
Shwachman-Bodian-Diamond Syndrome Protein3

External Ids:    HGNC: 194401   Entrez Gene: 511192   Ensembl: ENSG000001265247   OMIM: 6074445   UniProtKB: Q9Y3A53   

Export aliases for SBDS gene to outside databases

Previous GC identifers: GC07M065093 GC07M065850 GC07M065864 GC07M065896 GC07M066090 GC07M062635


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

Entrez Gene summary for SBDS Gene:
This gene encodes a member of a highly conserved protein family that exists from archaea to vertebrates and
plants. The encoded protein may function in RNA metabolism. Mutations within this gene are associated with
Shwachman-Bodian-Diamond syndrome. An alternative transcript has been described, but its biological nature has
not been determined. This gene has a closely linked pseudogene that is distally located. (provided by RefSeq, Jul
2008)

GeneCards Summary for SBDS Gene: 
SBDS (Shwachman-Bodian-Diamond syndrome) is a protein-coding gene. Diseases associated with SBDS include shwachman-diamond syndrome, and inherited bone marrow failure syndromes. GO annotations related to this gene include microtubule binding and rRNA binding.

UniProtKB/Swiss-Prot: SBDS_HUMAN, Q9Y3A5
Function: Required for the assembly of mature ribosomes and ribosome biogenesis. Together with EFTUD1, triggers
the GTP-dependent release of EIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for
translation competence by allowing 80S ribosome assembly and facilitating EIF6 recycling to the nucleus, where it
is required for 60S rRNA processing and nuclear export. Required for normal levels of protein synthesis. May play
a role in cellular stress resistance. May play a role in cellular response to DNA damage. May play a role in cell
proliferation

Gene Wiki entry for SBDS 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000007.13  NC_018918.2  NT_007933.15  NT_079593.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SBDS gene promoter:
         SRF   Elk-1   SRF (504 AA)   RREB-1   FOXO3   FOXO3b   GATA-1   RORalpha1   STAT3   FOXO3a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 3): SBDS promoter sequence
   Search SABiosciences Chromatin IP Primers for SBDS

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


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

Entrez Gene cytogenetic band: 7q11.21   Ensembl cytogenetic band:  7q11.21   HGNC cytogenetic band: 7q11.22

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

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M066452:  view genomic region     (about GC identifiers)

Start:
66,452,664 bp from pter      End:
66,460,588 bp from pter
Size:
7,925 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 65,790,252-65,798,150     

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SBDS_HUMAN, Q9Y3A5 (See protein sequence)
Recommended Name: Ribosome maturation protein SBDS  
Size: 250 amino acids; 28764 Da
Subunit: Associates with the 60S ribosomal subunit. Interacts with NPM1, RPA1 and PRKDC. May interact with NIP7
Subcellular location: Cytoplasm. Nucleus, nucleolus. Nucleus, nucleoplasm. Cytoplasm, cytoskeleton, spindle.
Note=Primarily detected in the cytoplasm, and at low levels in nucleus and nucleolus (PubMed:19602484 and
PubMed:17475909). Detected in the nucleolus during G1 and G2 phase of the cell cycle, and diffusely distributed
in the nucleus during S phase. Detected at the mitotic spindle. Colocalizes with the microtubule organizing
center during interphase (PubMed:19759903)
2 PDB 3D structures from and Proteopedia for SBDS:
2KDO (3D)        2L9N (3D)    
Secondary accessions: A8K0P4 Q96FX0 Q9NV53

Explore the universe of human proteins at neXtProt for SBDS: NX_Q9Y3A5

Explore proteomics data for SBDS at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y3A5

  • SBDS Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SBDS Protein Expression
    REFSEQ proteins: NP_057122.2  
    ENSEMBL proteins: 
     ENSP00000246868   ENSP00000394586  

    Human Recombinant Protein Products for SBDS: 
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    Novus Biologicals SBDS Proteins
    Novus Biologicals SBDS Lysate
    Sino Biological Recombinant Protein for SBDS
    Browse Sino Biological Cell Lysates 
    ProSpec Recombinant Protein for SBDS
    Cloud-Clone Corp. Proteins for SBDS 

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000922spindle pole IDA18324336
    GO:0005634nucleus IDA15860664
    GO:0005654nucleoplasm IEA--
    GO:0005730nucleolus IDA15860664
    GO:0005737cytoplasm IDA15860664

    SBDS for ontologies           About GeneDecksing



    SBDS Antibody Products: 
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    Cloud-Clone Corp. Antibodies for SBDS 
    ThermoFisher Antibody for SBDS
    LSBio Antibodies in human, mouse, rat for SBDS 

    Assay Products for SBDS: 
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    4 InterPro protein domains:
     IPR019783 Ribosome_mat_SBDS_N
     IPR018978 Ribosome_mat_SBDS_C
     IPR002140 Ribosome_maturation_pr_SBDS
     IPR018023 Ribosome_mat_SBDS_CS

    Graphical View of Domain Structure for InterPro Entry Q9Y3A5

    ProtoNet protein and cluster: Q9Y3A5

    1 Blocks protein domain: IPB002140 Protein of unknown function UPF0023

    UniProtKB/Swiss-Prot: SBDS_HUMAN, Q9Y3A5
    Similarity: Belongs to the SDO1/SBDS family


    SBDS 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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SBDS_HUMAN, Q9Y3A5
    Function: Required for the assembly of mature ribosomes and ribosome biogenesis. Together with EFTUD1, triggers
    the GTP-dependent release of EIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for
    translation competence by allowing 80S ribosome assembly and facilitating EIF6 recycling to the nucleus, where it
    is required for 60S rRNA processing and nuclear export. Required for normal levels of protein synthesis. May play
    a role in cellular stress resistance. May play a role in cellular response to DNA damage. May play a role in cell
    proliferation

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI17475909
    GO:0008017microtubule binding IDA18324336
    GO:0019843rRNA binding IDA17475909
    GO:0043022ribosome binding IDA--
         
    SBDS for ontologies           About GeneDecksing


    Phenotypes:
         13 MGI mutant phenotypes (inferred from 6 alleles(MGI details for Sbds):
     cardiovascular system  cellular  digestive/alimentary  embryogenesis  endocrine/exocrine gland 
     growth/size  hematopoietic system  homeostasis/metabolism  immune system  liver/biliary system 
     mortality/aging  normal  skeleton 

    SBDS for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for SBDS 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for SBDS

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

    miRNA
    Products:
        
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SBDS
    8/15 QIAGEN miScript miRNA Assays for microRNAs that regulate SBDS (see all 15):
    hsa-miR-140-5p hsa-miR-1271 hsa-miR-4255 hsa-miR-340 hsa-miR-103a hsa-miR-378b hsa-miR-422a hsa-miR-656
    SwitchGear 3'UTR luciferase reporter plasmidSBDS 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector: SBDS (NM_016038)
    Sino Biological Human cDNA Clone for SBDS
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SBDS
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SBDS
    Sirion Biotech Customized lentivirus for stable overexpression of SBDS 
                         Customized lentivirus expression plasmids for stable overexpression of SBDS 

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for SBDS
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SBDS


    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for SBDS About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Ribosome biogenesis in eukaryotes
    Ribosome biogenesis in eukaryotes

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways




    1         Kegg Pathway  (Kegg details for SBDS):
        Ribosome biogenesis in eukaryotes


    SBDS for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SBDS

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

    5/51 Interacting proteins for SBDS (Q9Y3A53 ENSP000002468684) via UniProtKB, MINT, STRING, and/or I2D (see all 51)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EFTUD1Q7Z2Z23, ENSP000002682064I2D: score=3 STRING: ENSP00000268206
    TPT1P136933, ENSP000003683504I2D: score=3 STRING: ENSP00000368350
    CLN3Q132863, ENSP000003530734I2D: score=2 STRING: ENSP00000353073
    DHX15O431433, ENSP000003367414I2D: score=2 STRING: ENSP00000336741
    EEF2P136393, ENSP000003079404I2D: score=1 STRING: ENSP00000307940
    About this table

    Gene Ontology (GO): 5/10 biological process terms (GO ID links to tree view) (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001833inner cell mass cell proliferation IEA--
    GO:0006364rRNA processing IMP17643419
    GO:0008283cell proliferation IMP19759903
    GO:0030282bone mineralization IMP17920346
    GO:0030595leukocyte chemotaxis IDA14743349

    SBDS for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SBDS

    1 HMDB Compound for SBDS    About this table
    CompoundSynonyms CAS #PubMed Ids
    Guanosine triphosphate5'-GTP (see all 10)86-01-1--

    Search CenterWatch for drugs/clinical trials and news about SBDS

    (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,
    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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SBDS gene: 
    NM_016038.2  

    Unigene Cluster for SBDS:

    Shwachman-Bodian-Diamond syndrome
    Hs.110445  [show with all ESTs]
    Unigene Representative Sequence: AY169963
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000246868(uc003tvm.1) ENST00000414306 ENST00000490953 ENST00000463579

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SBDS
    8/15 QIAGEN miScript miRNA Assays for microRNAs that regulate SBDS (see all 15):
    hsa-miR-140-5p hsa-miR-1271 hsa-miR-4255 hsa-miR-340 hsa-miR-103a hsa-miR-378b hsa-miR-422a hsa-miR-656
    SwitchGear 3'UTR luciferase reporter plasmidSBDS 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for SBDS
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SBDS
    Clone
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    OriGene clones in human, mouse for SBDS (see all 8)
    OriGene ORF clones in mouse, rat for SBDS
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SBDS (NM_016038)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SBDS
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SBDS
    Sirion Biotech Customized lentivirus for stable overexpression of SBDS 
                         Customized lentivirus expression plasmids for stable overexpression of SBDS 
    Primer
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    OriGene qPCR primer pairs and template standards for SBDS
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SBDS
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SBDS

    Additional mRNA sequence: 

    AF151855.1 AK001779.1 AK289609.1 AY169963.1 BC065700.1 

    15 DOTS entries:

    DT.100828046  DT.442442  DT.121116345  DT.100828036  DT.100031370  DT.100828026  DT.100828038  DT.100828027 
    DT.121057685  DT.121058023  DT.91900904  DT.102843941  DT.121057811  DT.121116324  DT.92454584 

    24/321 AceView cDNA sequences (see all 321):

    CR606525 CR606624 BM505370 BF337825 AW157607 BM471482 BM967238 AK001779 
    CA311264 BF726443 BM141988 BM784674 BM126186 CR612387 CR613195 CR604577 
    AW236671 AI572774 BU075955 CR596032 NM_016038 BG031467 CR599805 BM742953 

    GeneLoc Exon Structure

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

    ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5
    SP1:                                          
    SP2:              -                           


    ECgene alternative splicing isoforms for SBDS

    (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

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


    SBDS expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/26 selected tissues (see all 26) fully expand
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Testis (Reproductive System)    fully expand to see all 4 entries
             Leydig Cells Testis Interstitium
             seminal vesicle ; glandular cells   
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Colon (Gastrointestinal Tract)    fully expand to see all 3 entries
             rectum ; glandular cells   
     
     Pancreas (Endocrine System)    fully expand to see all 2 entries
             Islets of Langerhans
             pancreas ; exocrine glandular cells   

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

    SOURCE GeneReport for Unigene cluster: Hs.110445

    UniProtKB/Swiss-Prot: SBDS_HUMAN, Q9Y3A5
    Tissue specificity: Widely expressed

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

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SBDS

    (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 eukaryotes.

    Orthologs for SBDS gene from 9/27 species (see all 27)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sbds1 , 5 Shwachman-Bodian-Diamond syndrome homolog (human)1, 5 88.27(n)1
    97.2(a)1
      5 (68.97 cM)5
    667111  NM_023248.11  NP_075737.11 
     1302457315 
    chicken
    (Gallus gallus)
    Aves LOC1008583621 ribosome maturation protein SBDS-like 81.07(n)
    89.2(a)
      100858362  XM_003642388.1  XP_003642436.1 
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.119422 Xenopus laevis transcribed sequence with moderate similarity more 79.96(n)    48052620 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc567002 similar to Shwachman-Bodian-Diamond syndrome 78.48(n)   394096  BC050179.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG85491 CG8549 60.05(n)
    59.51(a)
      38749  NM_139800.2  NP_648057.2 
    worm
    (Caenorhabditis elegans)
    Secernentea sbds-11 Protein SBDS-1 58.5(n)
    57.14(a)
      175218  NM_064825.4  NP_497226.2 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SDO1(YLR022C)4
    SDO11
    Essential protein involved in 60S ribosome maturation; more4
    Sdo1p1
    51.88(n)1
    43.1(a)1
      12(184926-184174)4
    8507091, 4  NP_013122.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G438601 sequence-specific DNA binding transcription factor 57.59(n)
    51.63(a)
      840982  NM_103512.2  NP_564488.1 
    rice
    (Oryza sativa)
    Liliopsida Os08g01075001 hypothetical protein 55.33(n)
    51.87(a)
      4344458  NM_001067333.1  NP_001060798.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SBDS gene

    SBDS for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for SBDS
    PGOHUM00000233413


    (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) 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

    10/302 SNPs in SBDS are shown (see all 302)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
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    ----------
    VAR_0153944
    Shwachman-Diamond syndrome (SDS)4--see VAR_0153942 R T mis40--------
    VAR_0153924
    Shwachman-Diamond syndrome (SDS)4--see VAR_0153922 K E mis40--------
    VAR_0153914
    Shwachman-Diamond syndrome (SDS)4--see VAR_0153912 E G mis40--------
    VAR_0153954
    Shwachman-Diamond syndrome (SDS)4--see VAR_0153952 R C mis40--------
    VAR_0153934
    Shwachman-Diamond syndrome (SDS)4--see VAR_0153932 I S mis40--------
    rs793448181,2,4
    C,FShwachman-Diamond syndrome (SDS)4 non-pathogenic169932502(+) GGTCAA/GTCAGA 2 T I mis12Minor allele frequency- G:0.02NA EU 5859
    rs289420991,2,4
    CShwachman-Diamond syndrome (SDS)4 pathogenic169939407(-) ACCAAA/CCAGAT 2 K N mis10--------
    rs731516751,2
    C,Fnon-pathogenic169932486(+) TCTCGG/AAAGCA 2 /F syn14Minor allele frequency- A:0.04NA EU 5972
    rs10616951,2
    C,Fnon-pathogenic169938282(-) GCCAAA/GAAGGA 2 K syn1 trp35Minor allele frequency- G:0.09MN NA EU 6179
    rs1139939891,2
    C,Fnon-pathogenic169938342(-) GACCTC/TGATGA 2 L syn12Minor allele frequency- T:0.01NA EU 5871

    HapMap Linkage Disequilibrium report for SBDS (66452664 - 66460588 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for SBDS:    About this table     
    Variant IDTypeSubtypePubMed ID
    essv3137CNV CNV17122850
    dgv2091e1CNV Complex17122850


    Human Gene Mutation Database (HGMD): SBDS

    Locus Specific Mutation Databases (LSDB): SBDS
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing SBDS
    DNA2.0 Custom Variant and Variant Library Synthesis for SBDS

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 607444   
    OMIM disorders: 260400  
    UniProtKB/Swiss-Prot: SBDS_HUMAN, Q9Y3A5
  • Shwachman-Diamond syndrome (SDS) [MIM:260400]: Autosomal recessive disorder characterized by pancreatic
    exocrine insufficiency, hematologic dysfunction, and skeletal abnormalities. Note=The disease is caused by
    mutations affecting the gene represented in this entry

  • 17 diseases for SBDS:    About MalaCards
    shwachman-diamond syndrome    inherited bone marrow failure syndromes    exocrine pancreatic insufficiency    metaphyseal dysplasia
    aplastic anemia    batten disease    dyskeratosis congenita    common variable immunodeficiency
    neutropenia    autosomal recessive disease    type 1 diabetes mellitus    type 1 diabetes
    anemia    diabetes mellitus    myelodysplastic syndromes    pancreatitis
    leukemia

    4 diseases from the University of Copenhagen DISEASES database for SBDS:
    Exocrine pancreatic insufficiency     Neutropenia     Metaphyseal dysplasia     Autosomal recessive disease

    SBDS for disorders           About GeneDecksing

    4 Novoseek inferred disease relationships for SBDS gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    shwachman-diamond syndrome 98.5 25 17376717 (2), 18280855 (2), 19211642 (2), 15474150 (1) (see all 21)
    neutropenia 57.1 5 19211642 (1), 19759903 (1)
    anemia aplastic 54.3 1 17478638 (1)
    genetic disorder 52.8 1 19759903 (1)

    GeneTests: SBDS
    GeneReviews: SBDS
    Genetic Association Database (GAD): SBDS
    Human Genome Epidemiology (HuGE) Navigator: SBDS (3 documents)

    Export disorders for SBDS 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)
    About This Section

    PubMed articles for SBDS gene, integrated from 9 sources (see all 70):
    (articles sorted by number of sources associating them with SBDS)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations in SBDS are associated with Shwachman-Diamond syndrome. (PubMed id 12496757)1, 2, 3, 9 Boocock G.R.B.... Rommens J.M. (2003)
    2. The human Shwachman-Diamond syndrome protein, SBDS, associates with ribosomal RNA. (PubMed id 17475909)1, 2, 9 Ganapathi K.A....Shimamura A. (2007)
    3. SBDS expression and localization at the mitotic spind le in human myeloid progenitors. (PubMed id 19759903)1, 2, 9 Orelio C....Kuijpers T.W. (2009)
    4. The Shwachman-Diamond SBDS protein localizes to the nucleolus. (PubMed id 15860664)1, 2, 9 Austin K.M....Shimamura A. (2005)
    5. Mutations in the SBDS gene in acquired aplastic anemia. (PubMed id 17478638)1, 4, 9 Calado R.T....Young N.S. (2007)
    6. Structure, dynamics, and RNA interaction analysis of the human SBDS protein. (PubMed id 20053358)1, 2, 9 de Oliveira J.F....Zeri A.C. (2010)
    7. The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels. (PubMed id 17643419)1, 2, 9 Hesling C....Zanchin N.I. (2007)
    8. Shwachman-Bodian Diamond syndrome is a multi-function al protein implicated in cellular stress responses. (PubMed id 19602484)1, 2 Ball H.L....Myers J.S. (2009)
    9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    10. 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)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
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      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)
    About This Section
    Entrez Gene: 51119 HGNC: 19440 AceView: SBDS Ensembl:ENSG00000126524 euGenes: HUgn51119
    ECgene: SBDS Kegg: 51119 H-InvDB: SBDS

    (According to HUGE)
    About This Section
      --

    (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 SBDS Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SBDS Genetics and Cytogenetics in Oncology and Haematology
    SBDSbasehttp://bioinf.uta.fi/SBDSbase/
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SBDS

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

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



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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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