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SBDS Gene

protein-coding   GIFtS: 67
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)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 ribosome 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000007.14  NC_018918.2  NT_007933.16  
Regulatory elements:
   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 Chromatin IP Primers for SBDS

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 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, Cloud-Clone Corp, and/or others.)
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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
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: 

  • Ubiquitination2 at Lys62, Lys90, Lys98, Lys159
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins: NP_057122.2  
    ENSEMBL proteins: 
     ENSP00000246868   ENSP00000394586  

    SBDS Human Recombinant Protein Products:

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    Novus Biologicals SBDS Proteins
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    SBDS Antibody Products:

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    Abcam antibodies for SBDS
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    SBDS Assay Products:

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    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for SBDS
    Cloud-Clone Corp. CLIAs for SBDS


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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,
    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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    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): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI17475909
    GO:0008017microtubule binding IDA18324336
    GO:0019843rRNA binding IDA17475909
    GO:0043022ribosome binding IDA--
    GO:0044822poly(A) RNA 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/body  hematopoietic system  homeostasis/metabolism  immune system  liver/biliary system 
     mortality/aging  normal  skeleton 

    SBDS for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SBDS
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models 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:
        
    miRTarBase miRNAs that target SBDS:
    hsa-let-7c-5p (MIRT051786), hsa-mir-590-3p (MIRT016171)

    Block miRNA regulation of human, mouse, rat SBDS using miScript Target Protectors
    Selected qRT-PCR 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:
        
    OriGene RNAi products in human, mouse, rat for SBDS
    Predesigned siRNA for gene silencing in human, mouse, rat SBDS

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

    Clone
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    OriGene clones in human, mouse for SBDS (see all 7)
    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)
    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

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for SBDS 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SBDS


    (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
    SBDS_HUMAN, Q9Y3A5: 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)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton5
    nucleus5
    cytosol1

    Gene Ontology (GO): 5 cellular component terms:    About this table

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

    SBDS for ontologies           About GeneDecksing


    (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 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

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

        GeneGlobe Interaction Network for SBDS

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

    Selected Interacting proteins for SBDS (Q9Y3A53 ENSP000002468684) via UniProtKB, MINT, STRING, and/or I2D (see all 68)
    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): Selected biological process terms (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, 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 SBDS

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



    (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, Primers from OriGene, and/or QIAGEN )
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    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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    Block miRNA regulation of human, mouse, rat SBDS using miScript Target Protectors
    Selected qRT-PCR 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
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    OriGene RNAi products in human, mouse, rat for SBDS
    Predesigned siRNA for gene silencing in human, mouse, rat SBDS
    Clone
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    OriGene clones in human, mouse for SBDS (see all 7)
    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
    Primer
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    OriGene qPCR primer pairs and template standards for SBDS
    OriGene qSTAR qPCR primer pairs in human, mouse for SBDS
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SBDS
      QuantiTect SYBR Green Assays in human, mouse, rat SBDS
      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 

    Selected AceView cDNA sequences (see all 321):

    CA311264 BU683524 AW272239 AI467898 AW236671 CA448228 CR613995 AU154879 
    AI809949 AW302566 CR591576 BF844583 BM126186 AA932576 CR622210 AI471995 
    AA860575 BE221056 AI572774 BF941208 BU682067 CF126968 BC065700 AL550005 

    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™, 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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    SBDS expression in normal human tissues (normalized intensities)
    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
     selected tissues (see all 19) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
     
     Ovary (Reproductive System)
             Oviduct
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    SBDS Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SBDS Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.110445

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

        Custom PCR Arrays for SBDS
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    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)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for SBDS gene from Selected 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_003642388.2  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_001274553.1  NP_001261482.1 
    worm
    (Caenorhabditis elegans)
    Secernentea sbds-11 sbds-1 58.5(n)
    57.14(a)
      175218  NM_064825.5  NP_497226.2 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SDO1(YLR022C)4
    SDO11
    Essential protein involved in 60S ribosome maturation; more4
    SDO11
    53.36(n)1
    45.92(a)1
      12(184926-184174)4
    8507091, 4  NP_013122.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G438601 AT1G43860 57.3(n)
    51.24(a)
      840982  NM_103512.2  NP_564488.1 
    rice
    (Oryza sativa)
    Liliopsida Os08g01075001 Os08g0107500 54.22(n)
    50.21(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)
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    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), 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 SBDS (see all 302)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    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--------
    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--------
    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

    Site Specific Mutation Identification with 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, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    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

  • Selected diseases for SBDS (see all 24):    
    About MalaCards
    shwachman-diamond syndrome    inherited bone marrow failure syndromes    aplastic anemia    metaphyseal dysplasia
    exocrine pancreatic insufficiency    batten disease    autosomal recessive disease    dyskeratosis congenita
    common variable immunodeficiency    neutropenia    type 1 diabetes mellitus    type 1 diabetes
    osteoporosis    myelodysplastic syndromes    diabetes mellitus    tonsillitis
    pancreatitis    multiple myeloma    malaria    myeloma

    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)
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    PubMed articles for SBDS gene, integrated from 10 sources (see all 74):
    (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. (Nat. Genet. 2003)
    2. The human Shwachman-Diamond syndrome protein, SBDS, associates with ribosomal RNA. (PubMed id 17475909)1, 2, 9 Ganapathi K.A....Shimamura A. (Blood 2007)
    3. SBDS expression and localization at the mitotic spindle in human myeloid progenitors. (PubMed id 19759903)1, 2, 9 Orelio C....Kuijpers T.W. (PLoS ONE 2009)
    4. The Shwachman-Diamond SBDS protein localizes to the nucleolus. (PubMed id 15860664)1, 2, 9 Austin K.M.... Shimamura A. (Blood 2005)
    5. Mutations in the SBDS gene in acquired aplastic anemia. (PubMed id 17478638)1, 4, 9 Calado R.T....Young N.S. (Blood 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. (J. Mol. Biol. 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. (Exp. Cell Res. 2007)
    8. Shwachman-Bodian Diamond syndrome is a multi-functional protein implicated in cellular stress responses. (PubMed id 19602484)1, 2 Ball H.L....Myers J.S. (Hum. Mol. Genet. 2009)
    9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 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. (Genome Res. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 51119 HGNC: 19440 AceView: SBDS Ensembl:ENSG00000126524 euGenes: HUgn51119
    ECgene: SBDS Kegg: 51119 H-InvDB: SBDS

    (According to HUGE)
    About This Section

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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 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/books/NBK1116/?term=SBDS[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    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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