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Aliases for BEND3 Gene

Aliases for BEND3 Gene

  • BEN Domain Containing 3 2 3 5
  • KIAA1553 2 3 4

External Ids for BEND3 Gene

Previous HGNC Symbols for BEND3 Gene

  • KIAA1553

Previous GeneCards Identifiers for BEND3 Gene

  • GC06M107494
  • GC06M107386
  • GC06M104957

Summaries for BEND3 Gene

GeneCards Summary for BEND3 Gene

BEND3 (BEN Domain Containing 3) is a Protein Coding gene.

UniProtKB/Swiss-Prot for BEND3 Gene

  • Transcriptional repressor which associates with the NoRC (nucleolar remodeling complex) complex and plays a key role in repressing rDNA transcription. The sumoylated form modulates the stability of the NoRC complex component BAZ2A/TIP5 by controlling its USP21-mediated deubiquitination (PubMed:21914818, PubMed:26100909). Binds to unmethylated major satellite DNA and is involved in the recruitment of the Polycomb repressive complex 2 (PRC2) to major satellites (By similarity).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BEND3 Gene

Genomics for BEND3 Gene

Regulatory Elements for BEND3 Gene

Enhancers for BEND3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around BEND3 on UCSC Golden Path with GeneCards custom track

Genomic Location for BEND3 Gene

Chromosome:
6
Start:
107,065,180 bp from pter
End:
107,115,269 bp from pter
Size:
50,090 bases
Orientation:
Minus strand

Genomic View for BEND3 Gene

Genes around BEND3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BEND3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BEND3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BEND3 Gene

Proteins for BEND3 Gene

  • Protein details for BEND3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5T5X7-BEND3_HUMAN
    Recommended name:
    BEN domain-containing protein 3
    Protein Accession:
    Q5T5X7
    Secondary Accessions:
    • A2RRH2
    • Q9HCL9

    Protein attributes for BEND3 Gene

    Size:
    828 amino acids
    Molecular mass:
    94475 Da
    Quaternary structure:
    • Interacts with HDAC2 and HDAC3, but not HDAC1. Interacts with SALL4. Interacts with SMARCA5/SNF2H, BAZ2A/TIP5 and USP21. Interacts with the nucleosome remodeling and histone deacetylase (NuRD) repressor complex (By similarity).

neXtProt entry for BEND3 Gene

Proteomics data for BEND3 Gene at MOPED

Post-translational modifications for BEND3 Gene

  • Sumoylated at Lys-20 by SUMO1 and at Lys-512 by SUMO1, SUMO2 and SUMO3. Sumoylation probably occurs sequentially, with that of Lys-20 preceding that of Lys-512. It does not alter association with heterochromatin, but is required for the repression of transcription.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for BEND3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for BEND3 Gene

Domains & Families for BEND3 Gene

Gene Families for BEND3 Gene

Protein Domains for BEND3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for BEND3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q5T5X7

UniProtKB/Swiss-Prot:

BEND3_HUMAN :
  • The BEN domain 4 is necessary and sufficient for the localization of BEND3 to heterochromatic regions.
Domain:
  • The BEN domain 4 is necessary and sufficient for the localization of BEND3 to heterochromatic regions.
  • Contains 4 BEN domains.
genes like me logo Genes that share domains with BEND3: view

Function for BEND3 Gene

Molecular function for BEND3 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor which associates with the NoRC (nucleolar remodeling complex) complex and plays a key role in repressing rDNA transcription. The sumoylated form modulates the stability of the NoRC complex component BAZ2A/TIP5 by controlling its USP21-mediated deubiquitination (PubMed:21914818, PubMed:26100909). Binds to unmethylated major satellite DNA and is involved in the recruitment of the Polycomb repressive complex 2 (PRC2) to major satellites (By similarity).

Gene Ontology (GO) - Molecular Function for BEND3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000182 rDNA binding IDA 26100909
genes like me logo Genes that share ontologies with BEND3: view
genes like me logo Genes that share phenotypes with BEND3: view

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for BEND3 Gene

Localization for BEND3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BEND3 Gene

Nucleus. Nucleus, nucleolus. Note=In the nucleus, observed in heterochromatic foci containing CBX1, CBX3, CBX5 and histone H3 trimethylated at Lys-9. Released from chromatin during decondensation. Association with heterochromatin does not depend on sumoylation. {ECO:0000269 PubMed:21914818}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for BEND3 Gene COMPARTMENTS Subcellular localization image for BEND3 gene
Compartment Confidence
nucleus 5
cytosol 4
golgi apparatus 2

No data available for Gene Ontology (GO) - Cellular Components for BEND3 Gene

Pathways & Interactions for BEND3 Gene

SuperPathways for BEND3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for BEND3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA IMP 26100909
GO:0006306 DNA methylation IMP 26100909
GO:0006351 transcription, DNA-templated IEA --
GO:0034773 histone H4-K20 trimethylation IDA 26100909
GO:0036124 histone H3-K9 trimethylation IDA 26100909
genes like me logo Genes that share ontologies with BEND3: view

No data available for Pathways by source and SIGNOR curated interactions for BEND3 Gene

Drugs & Compounds for BEND3 Gene

No Compound Related Data Available

Transcripts for BEND3 Gene

mRNA/cDNA for BEND3 Gene

Unigene Clusters for BEND3 Gene

BEN domain containing 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for BEND3 Gene

No ASD Table

Relevant External Links for BEND3 Gene

GeneLoc Exon Structure for
BEND3
ECgene alternative splicing isoforms for
BEND3

Expression for BEND3 Gene

mRNA expression in normal human tissues for BEND3 Gene

Protein differential expression in normal tissues from HIPED for BEND3 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MOPED, and MaxQB for BEND3 Gene



SOURCE GeneReport for Unigene cluster for BEND3 Gene Hs.418045

mRNA Expression by UniProt/SwissProt for BEND3 Gene

Q5T5X7-BEND3_HUMAN
Tissue specificity: Expressed at least in heart, kidney, liver, ovary and spleen, with highest levels in spleen and lowest in heart. Expressed on the surface of T cells.
genes like me logo Genes that share expression patterns with BEND3: view

Protein tissue co-expression partners for BEND3 Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for BEND3 Gene

Orthologs for BEND3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for BEND3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia BEND3 35
  • 89.86 (n)
  • 93.84 (a)
BEND3 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia BEND3 35
  • 90.74 (n)
  • 93.72 (a)
BEND3 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Bend3 35
  • 86.34 (n)
  • 91.15 (a)
Bend3 16
Bend3 36
  • 91 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia BEND3 35
  • 99.36 (n)
  • 99.64 (a)
BEND3 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Bend3 35
  • 87.21 (n)
  • 92.01 (a)
oppossum
(Monodelphis domestica)
Mammalia BEND3 36
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves BEND3 35
  • 71.11 (n)
  • 77.72 (a)
BEND3 36
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia BEND3 36
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia bend3 35
  • 63.75 (n)
  • 69.38 (a)
zebrafish
(Danio rerio)
Actinopterygii bend3 35
  • 63.07 (n)
  • 62.63 (a)
bend3 36
  • 54 (a)
OneToOne
Species with no ortholog for BEND3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for BEND3 Gene

ENSEMBL:
Gene Tree for BEND3 (if available)
TreeFam:
Gene Tree for BEND3 (if available)

Paralogs for BEND3 Gene

Pseudogenes.org Pseudogenes for BEND3 Gene

genes like me logo Genes that share paralogs with BEND3: view

No data available for Paralogs for BEND3 Gene

Variants for BEND3 Gene

Sequence variations from dbSNP and Humsavar for BEND3 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1060369 -- 107,065,589(-) CTCCC(A/G)AGTGG utr-variant-3-prime
rs4946809 -- 107,074,290(+) cgtgc(C/T)tgtaa intron-variant
rs4946810 -- 107,099,066(+) TTAAA(A/C)AGTGA intron-variant
rs4946811 -- 107,099,312(+) AGACA(A/C)AGACA intron-variant
rs4946812 -- 107,110,484(+) TTGGA(A/G)AAGGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for BEND3 Gene

Variant ID Type Subtype PubMed ID
esv2732546 CNV Deletion 23290073
dgv87n68 CNV Loss 17160897
esv2732547 CNV Deletion 23290073
esv2732548 CNV Deletion 23290073
nsv521601 CNV Loss 19592680
esv1657137 CNV Deletion 17803354
dgv1063n67 CNV Gain 20364138
esv27390 CNV Loss 19812545

Variation tolerance for BEND3 Gene

Residual Variation Intolerance Score: 1.89% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.74; 33.08% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for BEND3 Gene

Disorders for BEND3 Gene

Relevant External Links for BEND3

Human Genome Epidemiology (HuGE) Navigator
BEND3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
BEND3

No disorders were found for BEND3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for BEND3 Gene

Publications for BEND3 Gene

  1. Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization. (PMID: 25600804) Shiheido H. … Shimizu J. (Biochem. Biophys. Res. Commun. 2015) 3 4 67
  2. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3
  3. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3
  4. BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase. (PMID: 26100909) Khan A. … Prasanth S.G. (Proc. Natl. Acad. Sci. U.S.A. 2015) 3
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3

Products for BEND3 Gene

Sources for BEND3 Gene

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