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Aliases for BEND3 Gene

Aliases for BEND3 Gene

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

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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F107653 2.3 Ensembl ENCODE 11.8 -541.4 -541351 6.6 PKNOX1 ATF1 ZFP64 ZNF133 SIN3A FEZF1 ZNF2 ZNF121 GATA2 FOS BEND3 PIR51849 GC06P107632
GH06F106509 1 ENCODE 20.4 +602.1 602127 7.3 PKNOX1 MLX WRNIP1 ZFP64 ZNF493 ARID4B SIN3A DMAP1 ZNF48 ZNF2 BEND3 AIM1 SOBP ATG5 QRSL1 LOC101927405 GC06P106528
GH06F107847 1.6 FANTOM5 Ensembl ENCODE 11.8 -733.1 -733132 1.2 SIN3A ARID4B DMAP1 ZNF48 ZNF2 GLIS2 ELK1 ZNF143 ZNF263 ZNF202 SEC63 BEND3 SCML4 ENSG00000280135
GH06F107027 1.1 ENCODE 11.9 +86.9 86904 1.6 PKNOX1 ARNT CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 CBX5 ZNF207 BEND3 C6orf203 RPL3P7 PIR49317
GH06F106324 1.1 ENCODE 11.8 +789.7 789709 2.4 HDGF CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 FOS ZNF263 BEND3 ATG5 ENSG00000283623
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around BEND3 on UCSC Golden Path with GeneCards custom track

Promoters for BEND3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001223704 -231 3001 ARID4B SIN3A DMAP1 ZNF48 ZNF2 ZNF121 GLIS2 ZNF143 ZNF263 SP3

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

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

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
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 21914818
genes like me logo Genes that share ontologies with BEND3: view
genes like me logo Genes that share phenotypes with BEND3: view

Animal Models for BEND3 Gene

MGI Knock Outs for BEND3:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
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 BEND3 gene
Compartment Confidence
nucleus 5
cytosol 4
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for BEND3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005720 nuclear heterochromatin IDA 21914818
GO:0005730 nucleolus IEA,IDA 26100909
genes like me logo Genes that share ontologies with BEND3: view

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:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 21914818
GO:0000183 chromatin silencing at rDNA IMP 26100909
GO:0006306 DNA methylation IMP 26100909
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
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

Transcripts for BEND3 Gene

mRNA/cDNA for BEND3 Gene

Unigene Clusters for BEND3 Gene

BEN domain containing 3:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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 from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for BEND3 Gene



Protein tissue co-expression partners for BEND3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of BEND3 Gene:

BEND3

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

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
chimpanzee
(Pan troglodytes)
Mammalia BEND3 34 35
  • 99.36 (n)
dog
(Canis familiaris)
Mammalia BEND3 34 35
  • 90.74 (n)
cow
(Bos Taurus)
Mammalia BEND3 34 35
  • 89.86 (n)
rat
(Rattus norvegicus)
Mammalia Bend3 34
  • 87.21 (n)
mouse
(Mus musculus)
Mammalia Bend3 34 16 35
  • 86.34 (n)
oppossum
(Monodelphis domestica)
Mammalia BEND3 35
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves BEND3 34 35
  • 71.11 (n)
lizard
(Anolis carolinensis)
Reptilia BEND3 35
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia bend3 34
  • 63.75 (n)
zebrafish
(Danio rerio)
Actinopterygii bend3 34 35
  • 63.07 (n)
Species where no ortholog for BEND3 was found in the sources mined by GeneCards:
  • 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
rs10080762 -- 107,099,913(+) caccc(C/T)ggctg intron-variant
rs10457158 -- 107,105,326(+) agatc(C/G)cgcca intron-variant
rs1060369 -- 107,065,589(-) CTCCC(A/G)AGTGG utr-variant-3-prime
rs10674719 -- 107,097,814(+) AAAAA(-/AA)ACCCC intron-variant
rs10684852 -- 107,071,390(+) CAGAG(-/ATTC)ATTCC intron-variant

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

Variant ID Type Subtype PubMed ID
nsv604445 CNV loss 21841781
nsv604441 CNV loss 21841781
nsv604440 CNV loss 21841781
nsv521601 CNV loss 19592680
esv3610291 CNV loss 21293372
esv27390 CNV loss 19812545
esv2732548 CNV deletion 23290073
esv2732547 CNV deletion 23290073
esv2732546 CNV deletion 23290073
esv1657137 CNV deletion 17803354
dgv87n68 CNV loss 17160897
dgv6135n100 CNV gain 25217958
dgv10897n54 CNV gain 21841781
dgv10896n54 CNV loss 21841781
dgv1063n67 CNV gain 20364138

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)

Relevant External Links for BEND3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
BEND3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot 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 64
  2. 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 4 64
  3. A BEN-domain-containing protein associates with heterochromatin and represses transcription. (PMID: 21914818) Sathyan K.M. … Prasanth S.G. (J. Cell. Sci. 2011) 3 4 64
  4. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10997877) Nagase T. … Ohara O. (DNA Res. 2000) 3 4 64
  5. BEND3 is involved in the human-specific repression of calreticulin: Implication for the evolution of higher brain functions in human. (PMID: 26481236) Aghajanirefah A. … Ohadi M. (Gene 2016) 3 64

Products for BEND3 Gene

Sources for BEND3 Gene

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