Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SBDS Gene

Aliases for SBDS Gene

  • SBDS, Ribosome Maturation Factor 2 3 5
  • SBDS, Ribosome Assembly Guanine Nucleotide Exchange Factor 2 3
  • Shwachman-Bodian-Diamond Syndrome Protein 4
  • Shwachman-Bodian-Diamond Syndrome 2
  • Ribosome Maturation Protein SBDS 3
  • CGI-97 3
  • SWDS 3
  • SDS 3

External Ids for SBDS Gene

Previous GeneCards Identifiers for SBDS Gene

  • GC07M065093
  • GC07M065850
  • GC07M065864
  • GC07M065896
  • GC07M066090
  • GC07M066452
  • GC07M062635

Summaries for SBDS Gene

Entrez Gene Summary for SBDS Gene

  • This gene encodes a highly conserved protein that plays an essential role in ribosome biogenesis. The encoded protein interacts with elongation factor-like GTPase 1 to disassociate eukaryotic initiation factor 6 from the late cytoplasmic pre-60S ribosomal subunit allowing assembly of the 80S subunit. Mutations within this gene are associated with the autosomal recessive disorder Shwachman-Bodian-Diamond syndrome. This gene has a closely linked pseudogene that is distally located. [provided by RefSeq, Jan 2017]

GeneCards Summary for SBDS Gene

SBDS (SBDS, Ribosome Maturation Factor) is a Protein Coding gene. Diseases associated with SBDS include Shwachman-Diamond Syndrome and Aplastic Anemia. Among its related pathways are Ribosome biogenesis in eukaryotes. Gene Ontology (GO) annotations related to this gene include rRNA binding.

UniProtKB/Swiss-Prot for SBDS Gene

  • Required for the assembly of mature ribosomes and ribosome biogenesis. Together with EFL1, 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

Additional gene information for SBDS Gene

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

Genomics for SBDS Gene

GeneHancer (GH) Regulatory Elements for SBDS Gene

Promoters and enhancers for SBDS Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07I066993 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 -0.2 -177 4.4 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 TYW1 SBDS ENSG00000229180 LOC100420547 ENSG00000244657 SPDYE21P TMEM248 RABGEF1 ENSG00000230189 STAG3L4
GH07I067019 Enhancer 0.8 ENCODE 0.3 -24.2 -24246 0.8 HDAC1 PKNOX1 TCF12 ATF7 SMARCA5 ELF1 ZEB2 ZNF592 ATF4 SMARCA4 TYW1 LOC100420547 ENSG00000229180 ENSG00000273448 TMEM248 SBDS ENSG00000233383
GH07I067042 Enhancer 1.1 Ensembl ENCODE dbSUPER 0.2 -47.6 -47554 1.7 HDAC1 MEIS2 PKNOX1 ZBTB6 CEBPG NFE2 SMARCE1 SOX6 CEBPB CBFA2T3 LINC01372 TYW1 ENSG00000233383 SBDS
GH07I067035 Enhancer 0.7 ENCODE dbSUPER 0.3 -40.9 -40939 1.7 OSR2 ZFP69B KLF1 ZNF692 GLIS1 STAG3L4 TYW1 LOC100996437 SBDS ENSG00000233383
GH07I067024 Enhancer 0.6 Ensembl ENCODE dbSUPER 0.3 -30.0 -30020 1.6 STAG3L4 PMS2P4 TYW1 SBDS ENSG00000233383
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SBDS on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SBDS gene promoter:

Genomic Locations for SBDS Gene

Genomic Locations for SBDS Gene
chr7:66,987,677-66,995,601
(GRCh38/hg38)
Size:
7,925 bases
Orientation:
Minus strand
chr7:66,452,664-66,460,588
(GRCh37/hg19)

Genomic View for SBDS Gene

Genes around SBDS on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SBDS Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SBDS Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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 (PubMed:17643419). Found in a complex consisting of the 60S ribosomal subunit, SBDS and EFL1 (PubMed:26479198). Interacts with EFL1 (PubMed:25991726).

    Three dimensional structures from OCA and Proteopedia for SBDS Gene

neXtProt entry for SBDS Gene

Post-translational modifications for SBDS Gene

  • Ubiquitination at isoforms=62, posLast=9090, isoforms=98, and posLast=159159

Other Protein References for SBDS Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SBDS Gene

Domains & Families for SBDS Gene

Gene Families for SBDS Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for SBDS Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y3A5

UniProtKB/Swiss-Prot:

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

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 EFL1, 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:0003723 RNA binding IDA,HDA 22658674
GO:0005515 protein binding IPI 17475909
GO:0008017 microtubule binding IDA 18324336
GO:0019843 rRNA binding IDA 17475909
GO:0043022 ribosome binding IDA 21536732
genes like me logo Genes that share ontologies with SBDS: view
genes like me logo Genes that share phenotypes with SBDS: view

Human Phenotype Ontology for SBDS Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SBDS Gene

MGI Knock Outs for SBDS:

miRNA for SBDS Gene

miRTarBase miRNAs that target SBDS

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SBDS gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 5
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleus (3)
See all subcellular structures

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,IEA 15860664
GO:0005737 cytoplasm IEA,IDA 15860664
genes like me logo Genes that share ontologies with SBDS: view

Pathways & Interactions for SBDS Gene

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

Pathways by source for SBDS Gene

1 KEGG pathway for SBDS Gene

SIGNOR curated interactions for SBDS Gene

Activates:

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:0007052 mitotic spindle organization IDA 18324336
GO:0008283 cell proliferation IMP 19759903
GO:0030282 bone mineralization IMP 17920346
genes like me logo Genes that share ontologies with SBDS: view

Drugs & Compounds for SBDS Gene

(1) Drugs for SBDS Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0
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:

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for SBDS Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SBDS Gene



Protein tissue co-expression partners for SBDS Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SBDS Gene:

SBDS

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.

Evidence on tissue expression from TISSUES for SBDS Gene

  • Nervous system(4.9)
  • Liver(4.5)
  • Blood(4.4)
  • Bone marrow(3)
  • Heart(2.7)
  • Pancreas(2.7)
  • Muscle(2.6)
  • Stomach(2.2)
  • Kidney(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SBDS Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • ear
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
Pelvis:
  • pelvis
  • ureter
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • bone marrow
  • coagulation system
  • hair
  • red blood cell
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with SBDS: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein differential expression in normal tissues for SBDS Gene

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 33 34
  • 99.6 (n)
oppossum
(Monodelphis domestica)
Mammalia SBDS 34
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SBDS 34
  • 93 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SBDS 33 34
  • 92.13 (n)
dog
(Canis familiaris)
Mammalia SBDS 33 34
  • 90.09 (n)
mouse
(Mus musculus)
Mammalia Sbds 33 16 34
  • 88.27 (n)
rat
(Rattus norvegicus)
Mammalia Sbds 33
  • 86.67 (n)
chicken
(Gallus gallus)
Aves SBDS 33 34 34
  • 81.07 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia sbds 33
  • 77.33 (n)
Str.16646 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.11942 33
zebrafish
(Danio rerio)
Actinopterygii sbds 33 34
  • 75.61 (n)
zgc56700 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4209 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007882 33
  • 64.11 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG8549 33 34
  • 60.05 (n)
worm
(Caenorhabditis elegans)
Secernentea sbds-1 33 34
  • 58.5 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SDO1 33 34 36
  • 53.36 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAL154C 33
  • 51.94 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F15532g 33
  • 51.53 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G43860 33
  • 57.3 (n)
rice
(Oryza sativa)
Liliopsida Os08g0107500 33
  • 54.22 (n)
barley
(Hordeum vulgare)
Liliopsida Hv.1323 33
wheat
(Triticum aestivum)
Liliopsida Ta.9185 33
corn
(Zea mays)
Liliopsida Zm.9577 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 67 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sdo1 33
  • 54.77 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU00476 33
  • 54.53 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8625 33
Species where no ortholog for SBDS was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1061695 benign, Shwachman syndrome, not specified 66,994,269(-) T/C coding_sequence_variant, synonymous_variant
rs113993989 benign, Shwachman syndrome, not specified 66,994,329(-) G/A coding_sequence_variant, synonymous_variant
rs113993990 pathogenic, Shwachman syndrome, not provided 66,995,298(-) CC/C coding_sequence_variant, frameshift
rs113993991 pathogenic, Shwachman syndrome, not provided 66,994,286(-) TA/AG coding_sequence_variant, stop_gained
rs113993992 pathogenic, Shwachman syndrome, not provided 66,994,211(-) C/G splice_donor_variant

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

Variant ID Type Subtype PubMed ID
esv2759535 CNV gain 17122850
esv3571892 CNV loss 25503493
esv3891136 CNV gain 25118596
nsv1032575 CNV gain 25217958
nsv966836 CNV duplication 23825009

Variation tolerance for SBDS Gene

Residual Variation Intolerance Score: 34.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.89; 48.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SBDS Gene

Human Gene Mutation Database (HGMD)
SBDS
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SBDS

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SBDS Gene

Disorders for SBDS Gene

MalaCards: The human disease database

(4) MalaCards diseases for SBDS Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
shwachman-diamond syndrome
  • sds
aplastic anemia
  • aplastic anemia, susceptibility to
pulmonary fibrosis and/or bone marrow failure, telomere-related, 2
  • pulmonary fibrosis, idiopathic
inherited bone marrow failure syndromes
  • bmfs
- elite association - COSMIC cancer census association via MalaCards
Search SBDS in MalaCards View complete list of genes associated with diseases

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:21536732, ECO:0000269 PubMed:24898207}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SBDS

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SBDS: view

No data available for Genatlas for SBDS Gene

Publications for SBDS Gene

  1. Mutations in SBDS are associated with Shwachman-Diamond syndrome. (PMID: 12496757) Boocock GR … Rommens JM (Nature genetics 2003) 2 3 4 22 58
  2. Structure, dynamics, and RNA interaction analysis of the human SBDS protein. (PMID: 20053358) de Oliveira JF … Zeri AC (Journal of molecular biology 2010) 3 4 22 58
  3. SBDS expression and localization at the mitotic spindle in human myeloid progenitors. (PMID: 19759903) Orelio C … Kuijpers TW (PloS one 2009) 3 4 22 58
  4. The human Shwachman-Diamond syndrome protein, SBDS, associates with ribosomal RNA. (PMID: 17475909) Ganapathi KA … Shimamura A (Blood 2007) 3 4 22 58
  5. The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels. (PMID: 17643419) Hesling C … Zanchin NI (Experimental cell research 2007) 3 4 22 58

Products for SBDS Gene

Sources for SBDS Gene

Content
Loading form....