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BEND3 Gene(Protein Coding)

BEN Domain Containing 3

GCID:
GC06M107066
GIFtS:
40
Genes Participants
UDN Logo

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). Stimulates the ERCC6L translocase and ATPase activities (PubMed:28977671).

Additional gene information for BEND3 Gene

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

Genomics for BEND3 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for BEND3 Gene

Promoters and enhancers for BEND3 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
GH06I107113 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 550.8 -0.1 -127 3.8 ARID4B SIN3A DMAP1 ZNF2 POLR2B ZNF213 ZNF207 ZNF143 SP3 MXD4 BEND3 RNU6-1299P
GH06I107108 Promoter/Enhancer 0.9 EPDnew dbSUPER 550.4 +6.7 6660 0.1 USF1 CEBPB BEND3 GC06M107103
GH06I106509 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 20.4 +601.9 601925 7.7 PKNOX1 MLX ZNF493 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF48 ETS1 BEND3 SOBP ATG5 CRYBG1 QRSL1 LOC101927405 GC06P106528
GH06I106324 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 11.8 +789.7 789709 2.4 HDGF SMAD1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B CBX5 ATG5 BEND3 RNU6-344P
GH06I107654 Enhancer 1.8 UCNEbase Ensembl ENCODE dbSUPER 11.8 -542.0 -541996 5.3 PKNOX1 ZNF133 FEZF1 ZNF2 IRF4 ZNF121 ZNF213 ZNF143 ZNF207 ATF7 BEND3 PIR51849 GC06P107632 SOBP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around BEND3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BEND3 gene promoter:

Genomic Locations for BEND3 Gene

Genomic Locations for BEND3 Gene
chr6:107,065,180-107,115,269
(GRCh38/hg38)
Size:
50,090 bases
Orientation:
Minus strand
chr6:107,386,385-107,436,473
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for BEND3 Gene

Proteins for BEND3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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:
    • Homooligomer, probably a homooctamer (PubMed:28977671). Interacts with HDAC2 and HDAC3, but not HDAC1. Interacts with SALL4 (PubMed:21914818). Interacts with SMARCA5/SNF2H, BAZ2A/TIP5 and USP21 (PubMed:26100909). Interacts with the nucleosome remodeling and histone deacetylase (NuRD) repressor complex (By similarity). Interacts (via BEN domains 1 and 3) with ERCC6L (via N-terminal TPR repeat); the interaction is direct (PubMed:28977671).

    Three dimensional structures from OCA and Proteopedia for BEND3 Gene

neXtProt entry for BEND3 Gene

Protein Expression for BEND3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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.
genes like me logo Genes that share domains with BEND3: view

Function for BEND3 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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). Stimulates the ERCC6L translocase and ATPase activities (PubMed:28977671).

Phenotypes From GWAS Catalog for BEND3 Gene

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

Clone 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for BEND3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005720 nuclear heterochromatin IDA,IEA 21914818
GO:0005730 nucleolus IDA,IEA 26100909
genes like me logo Genes that share ontologies with BEND3: view

Pathways & Interactions for BEND3 Gene

SuperPathways for BEND3 Gene

PathCards logo More details on SuperPathways for BEND3
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 by RNA polymerase II IDA 21914818
GO:0000183 chromatin silencing at rDNA IEA,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

Drugs & Compounds for BEND3 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for BEND3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for BEND3 Gene

(5) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(55) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for BEND3 Gene

BEN domain containing 3:
Representative Sequences:

Clone 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

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BEND3 Gene

mRNA expression in normal human tissues for BEND3 Gene
mRNA expression by GTEx for BEND3 GenemRNA expression by BioGPS 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, PaxDb, 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.

Evidence on tissue expression from TISSUES for BEND3 Gene

  • Heart(2)
genes like me logo Genes that share expression patterns with BEND3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.36 (n)
dog
(Canis familiaris)
 Mammalia BEND3 33 34
  • 90.74 (n)
cow
(Bos Taurus)
 Mammalia BEND3 33 34
  • 89.86 (n)
rat
(Rattus norvegicus)
 Mammalia Bend3 33
  • 87.21 (n)
mouse
(Mus musculus)
 Mammalia Bend3 33 16 34
  • 86.34 (n)
oppossum
(Monodelphis domestica)
 Mammalia BEND3 34
  • 83 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves BEND3 33 34
  • 71.11 (n)
lizard
(Anolis carolinensis)
 Reptilia BEND3 34
  • 66 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia bend3 33
  • 63.75 (n)
zebrafish
(Danio rerio)
 Actinopterygii bend3 33 34
  • 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

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for BEND3 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000026691 -- 107,094,391(-) G/T intron_variant
rs1000243690 -- 107,100,839(-) G/T intron_variant
rs1000364027 -- 107,076,863(-) C/T intron_variant
rs1000487326 -- 107,071,199(-) C/T intron_variant
rs1000551399 -- 107,110,896(-) G/A genic_upstream_transcript_variant, intron_variant

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

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

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)

Additional Variant Information for BEND3 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BEND3 Gene

Disorders for BEND3 Gene

Additional Disease Information for BEND3

Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

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. A novel TPR-BEN domain interaction mediates PICH-BEND3 association. (PMID: 28977671) Pitchai GP … Hickson ID (Nucleic acids research 2017) 3 4 58
  2. Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization. (PMID: 25600804) Shiheido H … Shimizu J (Biochemical and biophysical research communications 2015) 3 4 58
  3. BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase. (PMID: 26100909) Khan A … Prasanth SG (Proceedings of the National Academy of Sciences of the United States of America 2015) 3 4 58
  4. A BEN-domain-containing protein associates with heterochromatin and represses transcription. (PMID: 21914818) Sathyan KM … Prasanth SG (Journal of cell science 2011) 3 4 58
  5. 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 research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4 58

Products for BEND3 Gene

Sources for BEND3 Gene

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