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Aliases for SBDS Gene

Aliases for SBDS Gene

  • Shwachman-Bodian-Diamond Syndrome 2 3
  • SDS 3 6
  • Shwachman-Bodian-Diamond Syndrome Protein 4
  • Ribosome Maturation Protein SBDS 3
  • CGI-97 3
  • SWDS 3

External Ids for SBDS Gene

Summaries for SBDS Gene

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-bodian-diamond syndrome and inherited bone marrow failure syndromes. Among its related pathways are Carbon metabolism and Metabolism. GO annotations related to this gene include microtubule binding and ribosome binding.

UniProtKB/Swiss-Prot for SBDS Gene

  • 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SBDS Gene

Genomics for SBDS Gene

Genomic Location for SBDS Gene

Start:
66,987,677 bp from pter
End:
66,995,601 bp from pter
Size:
7,925 bases
Orientation:
Minus strand

Genomic View for SBDS Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SBDS Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SBDS Gene

Regulatory Elements for SBDS Gene

Proteins for SBDS Gene

  • Protein details for SBDS Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y3A5-SBDS_HUMAN
    Recommended name:
    Ribosome maturation protein SBDS
    Protein Accession:
    Q9Y3A5
    Secondary Accessions:
    • A8K0P4
    • Q96FX0
    • Q9NV53

    Protein attributes for SBDS Gene

    Size:
    250 amino acids
    Molecular mass:
    28764 Da
    Quaternary structure:
    • Associates with the 60S ribosomal subunit. Interacts with NPM1, RPA1 and PRKDC. May interact with NIP7.

    Three dimensional structures from OCA and Proteopedia for SBDS Gene

neXtProt entry for SBDS Gene

Proteomics data for SBDS Gene at MOPED

Post-translational modifications for SBDS Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys62, Lys90, Lys98, and Lys159

Other Protein References for SBDS Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SBDS Gene

Domains for SBDS Gene

UniProtKB/Swiss-Prot:

SBDS_HUMAN
Family:
  • Belongs to the SDO1/SBDS family.:
    • Q9Y3A5
genes like me logo Genes that share domains with SBDS: view

No data available for Gene Families for SBDS Gene

Function for SBDS Gene

Molecular function for SBDS Gene

UniProtKB/Swiss-Prot 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) - Molecular Function for SBDS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17475909
GO:0008017 microtubule binding IDA 18324336
GO:0019843 rRNA binding IDA 17475909
GO:0043022 ribosome binding IDA 21536732
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with SBDS: view
genes like me logo Genes that share phenotypes with SBDS: view

miRNA for SBDS Gene

miRTarBase miRNAs that target SBDS

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for SBDS Gene

Localization for SBDS Gene

Subcellular locations from UniProtKB/Swiss-Prot for SBDS Gene

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). {ECO:0000269 PubMed:19759903}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SBDS Gene COMPARTMENTS Subcellular localization image for SBDS gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for SBDS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000922 spindle pole IDA 18324336
GO:0005634 nucleus IDA 15860664
GO:0005654 nucleoplasm IEA --
GO:0005730 nucleolus IDA 15860664
GO:0005737 cytoplasm IDA --
genes like me logo Genes that share ontologies with SBDS: view

Pathways for SBDS Gene

genes like me logo Genes that share pathways with SBDS: view

Gene Ontology (GO) - Biological Process for SBDS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001833 inner cell mass cell proliferation IEA --
GO:0006364 rRNA processing IMP 17643419
GO:0008283 cell proliferation IMP 19759903
GO:0030282 bone mineralization IMP 17920346
GO:0030595 leukocyte chemotaxis IDA 14743349
genes like me logo Genes that share ontologies with SBDS: view

Compounds for SBDS Gene

(1) HMDB Compounds for SBDS Gene

Compound Synonyms Cas Number PubMed IDs
Guanosine triphosphate
  • 5'-GTP
86-01-1
genes like me logo Genes that share compounds with SBDS: view

Transcripts for SBDS Gene

Unigene Clusters for SBDS Gene

Shwachman-Bodian-Diamond syndrome:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SBDS Gene

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

Relevant External Links for SBDS Gene

GeneLoc Exon Structure for
SBDS
ECgene alternative splicing isoforms for
SBDS

Expression for SBDS Gene

mRNA expression in normal human tissues for SBDS Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SBDS Gene

SOURCE GeneReport for Unigene cluster for SBDS Gene Hs.110445

mRNA Expression by UniProt/SwissProt for SBDS Gene

Q9Y3A5-SBDS_HUMAN
Tissue specificity: Widely expressed
genes like me logo Genes that share expressions with SBDS: view

Orthologs for SBDS Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SBDS Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SBDS 36
  • 99.6 (n)
  • 100 (a)
SBDS 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SBDS 36
  • 92.13 (n)
  • 98.8 (a)
SBDS 37
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SBDS 36
  • 90.09 (n)
  • 97.99 (a)
SBDS 37
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sbds 36
  • 88.27 (n)
  • 97.2 (a)
Sbds 16
Sbds 37
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SBDS 37
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SBDS 37
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sbds 36
  • 86.67 (n)
  • 97.2 (a)
chicken
(Gallus gallus)
Aves LOC100858362 36
  • 81.07 (n)
  • 89.2 (a)
SBDS 37
  • 89 (a)
OneToMany
SBDS 37
  • 79 (a)
OneToMany
African clawed frog
(Xenopus laevis)
Amphibia Xl.11942 36
tropical clawed frog
(Silurana tropicalis)
Amphibia sbds 36
  • 77.33 (n)
  • 86.4 (a)
Str.16646 36
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4209 36
zebrafish
(Danio rerio)
Actinopterygii sbds 36
  • 75.61 (n)
  • 82.68 (a)
sbds 37
  • 82 (a)
OneToOne
zgc56700 36
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007882 36
  • 64.11 (n)
  • 67.34 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG8549 36
  • 60.05 (n)
  • 59.51 (a)
CG8549 37
  • 58 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea sbds-1 36
  • 58.5 (n)
  • 57.14 (a)
sbds-1 37
  • 55 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAL154C 36
  • 51.94 (n)
  • 43.75 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SDO1 36
  • 53.36 (n)
  • 45.92 (a)
SDO1 37
  • 43 (a)
OneToOne
SDO1 39
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F15532g 36
  • 51.53 (n)
  • 45.42 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G43860 36
  • 57.3 (n)
  • 51.24 (a)
barley
(Hordeum vulgare)
Liliopsida Hv.1323 36
corn
(Zea mays)
Liliopsida Zm.9577 36
rice
(Oryza sativa)
Liliopsida Os08g0107500 36
  • 54.22 (n)
  • 50.21 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.9185 36
bread mold
(Neurospora crassa)
Ascomycetes NCU00476 36
  • 54.53 (n)
  • 49.79 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sdo1 36
  • 54.77 (n)
  • 51.04 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8625 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 67 (a)
OneToOne
Species with no ortholog for SBDS:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for SBDS Gene

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

Paralogs for SBDS Gene

Pseudogenes.org Pseudogenes for SBDS Gene

genes like me logo Genes that share paralogs with SBDS: view

No data available for Paralogs for SBDS Gene

Variants for SBDS Gene

Sequence variations from dbSNP and Humsavar for SBDS Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type MAF
rs1053594 -- 66,988,112(-) CTACT(C/T)TGTCT utr-variant-3-prime
rs1053607 -- 66,988,004(-) TATAC(A/G)ACAAA utr-variant-3-prime
rs1061695 Benign 66,994,269(-) GCCAA(A/G)AAGGA reference, synonymous-codon
rs4307226 -- 66,994,128(+) CTCCA(A/G)AAAAA intron-variant
rs4308614 -- 66,994,566(+) CTCGG(C/G)TCACT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SBDS Gene

Variant ID Type Subtype PubMed ID
essv3137 CNV CNV 17122850
dgv2091e1 CNV Complex 17122850

Relevant External Links for SBDS Gene

HapMap Linkage Disequilibrium report
SBDS
Human Gene Mutation Database (HGMD)
SBDS
Locus Specific Mutation Databases (LSDB)
SBDS

Disorders for SBDS Gene

(1) OMIM Diseases for SBDS Gene (607444)

UniProtKB/Swiss-Prot

SBDS_HUMAN
  • Shwachman-Diamond syndrome (SDS) [MIM:260400]: Autosomal recessive disorder characterized by pancreatic exocrine insufficiency, hematologic dysfunction, and skeletal abnormalities. {ECO:0000269 PubMed:12496757, ECO:0000269 PubMed:24898207}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(4) Novoseek inferred disease relationships for SBDS Gene

Disease -log(P) Hits PubMed IDs
shwachman-diamond syndrome 98.5 24
neutropenia 57.1 2
anemia aplastic 54.3 1
genetic disorder 52.8 1

Relevant External Links for SBDS

GeneTests
SBDS
GeneReviews
SBDS
Genetic Association Database (GAD)
SBDS
Human Genome Epidemiology (HuGE) Navigator
SBDS
genes like me logo Genes that share disorders with SBDS: view

Publications for SBDS Gene

  1. Mutations in SBDS are associated with Shwachman-Diamond syndrome. (PMID: 12496757) Boocock G.R.B. … Rommens J.M. (Nat. Genet. 2003) 2 3 4 23
  2. SBDS expression and localization at the mitotic spindle in human myeloid progenitors. (PMID: 19759903) Orelio C. … Kuijpers T.W. (PLoS ONE 2009) 3 4 23
  3. Structure, dynamics, and RNA interaction analysis of the human SBDS protein. (PMID: 20053358) de Oliveira J.F. … Zeri A.C. (J. Mol. Biol. 2010) 3 4 23
  4. The Shwachman-Diamond SBDS protein localizes to the nucleolus. (PMID: 15860664) Austin K.M. … Shimamura A. (Blood 2005) 3 4 23
  5. The human Shwachman-Diamond syndrome protein, SBDS, associates with ribosomal RNA. (PMID: 17475909) Ganapathi K.A. … Shimamura A. (Blood 2007) 3 4 23

Products for SBDS Gene

Sources for SBDS Gene

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