Aliases for BEND3 Gene
Aliases for BEND3 Gene
External Ids for BEND3 Gene
- HGNC: 23040
- Entrez Gene: 57673
- Ensembl: ENSG00000178409
- OMIM: 616374
- UniProtKB: Q5T5X7
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).
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
GeneHancer (GH) Regulatory Elements for BEND3 Gene
Promoters and enhancers for BEND3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)
GeneHancers around BEND3 on UCSC Golden Path with GeneCards custom track
- Top Transcription factor binding sites by QIAGEN in the BEND3 gene promoter:
-
- RSRFC4
- POU6F1 (c2)
- RFX1
- p53
- aMEF-2
- MEF-2A
- CBF(2)
- CBF-A
- CP1A
- NF-Y
Regulatory Element Products
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)
- Size:
- 50,089 bases
- Orientation:
- Minus strand
Genomic View for BEND3 Gene
Genes around BEND3 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 6q21 by Entrez Gene
- 6q21 by HGNC
- 6q21 by Ensembl
BEND3 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene 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
- 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).
Protein Expression 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
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
-
Custom Antibody ServicesOriGene Antibodies for BEND3
- Novus Biologicals Antibodies for BEND3
- Invitrogen Antibodies for BEND3 (AFLGC-BEND3)
- GeneTex BEND3 Antibody for BEND3
Protein Products
-
OriGene Purified Proteins for BEND3
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- Search GeneTex for Proteins for BEND3
Assay Products
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
Q5T5X7UniProtKB/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.
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). Stimulates the ERCC6L translocase and ATPase activities (PubMed:28977671).
Phenotypes From GWAS Catalog 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 |
Phenotypes for BEND3 Gene
- MGI mutant phenotypes for BEND3:
- inferred from 1 alleles
- GenomeRNAi human phenotypes for BEND3:
Animal Models for BEND3 Gene
- MGI Knock Outs for BEND3:
-
- Bend3 Bend3<tm1b(KOMP)Mbp>
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
- Cyagen custom Knockout/knockin (KOKI) mouse models for BEND3
-
CRISPR Products
-
OriGene CRISPR knockouts for BEND3
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- Overview of 55 available BEND3 gene related products
- Applied Biological Materials CRISPR for BEND3
-
Vectors and viruses for KO, Activation, Repression, and more
-
Santa Cruz Biotechnology (SCBT) CRISPR for BEND3
- GenScript: Design CRISPR guide RNA sequences for BEND3
miRNA for BEND3 Gene
- miRTarBase miRNAs that target BEND3
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for BEND3
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- genomics-online: shRNA clones - Search results for 55 available BEND3 gene related products
- Overview of 55 available BEND3 gene related products
Clone Products
- Sino Biological Human cDNA Clone for BEND3
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for BEND3
- Applied Biological Materials Clones for BEND3
-
Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
Cell Line Products
-
Horizon Cell Lines for BEND3
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}.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| cytosol | 4 |
| golgi apparatus | 2 |
- Nucleoplasm (2)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IEA | -- |
| GO:0005654 | nucleoplasm | IDA | -- |
| GO:0005720 | nuclear heterochromatin | IDA | 21914818 |
| GO:0005730 | nucleolus | IDA,IEA | 26100909 |
Pathways & Interactions for BEND3 Gene
No Data Available
Interacting Proteins for BEND3 Gene
Selected Interacting proteins:
Q5T5X7-BEND3_HUMAN
ENSP00000358038
for BEND3 Gene via
UniProtKB
MINT
STRING
IID
GPS-Prot Interaction Network for BEND3
| 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 | IMP | 26100909 |
| GO:0006306 | DNA methylation | IMP | 26100909 |
| GO:0006325 | chromatin organization | IEA | -- |
| GO:0006351 | transcription, DNA-templated | IEA | -- |
No data available for Pathways by source and SIGNOR curated interactions for BEND3 Gene
Transcripts for BEND3 Gene
mRNA/cDNA for BEND3 Gene
- (4) REFSEQ mRNAs :
- (3) Additional mRNA sequences :
- (55) Selected AceView cDNA sequences:
- (2) Ensembl transcripts including schematic representations, and UCSC links where relevant :
-
- ENST00000369042 6200 bps (uc063qjz.1)
- ENST00000429433 6654 bps (uc003prs.3)
Unigene Clusters for BEND3 Gene
- BEN domain containing 3:
- Representative Sequences:
CRISPR Products
-
OriGene CRISPR knockouts for BEND3
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for BEND3
- genomics-online: gRNA clones - Search results for 55 available BEND3 gene related products
- Overview of 55 available BEND3 gene related products
- Applied Biological Materials CRISPR for BEND3
-
Vectors and viruses for KO, Activation, Repression, and more
-
Santa Cruz Biotechnology (SCBT) CRISPR for BEND3
- GenScript: Design CRISPR guide RNA sequences for BEND3
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for BEND3
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- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for BEND3
- genomics-online: shRNA clones - Search results for 55 available BEND3 gene related products
- Overview of 55 available BEND3 gene related products
Clone Products
- Sino Biological Human cDNA Clone for BEND3
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for BEND3
- Applied Biological Materials Clones for BEND3
-
Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
Expression 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
- Elite partner
NURSA nuclear receptor signaling pathways regulating expression of BEND3 Gene:
BEND3SOURCE GeneReport for Unigene cluster for BEND3 Gene:
Hs.418045mRNA 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)
- Nervous system(2)
Primer Products
-
OriGene qPCR primer pairs for BEND3
- genomics-online: primer clones - Search results for 55 available BEND3 gene related products
- Overview of 55 available BEND3 gene related products
Gene Expression Assay Products
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.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | BEND3 34 33 |
|
OneToOne | |
| dog (Canis familiaris) |
Mammalia | BEND3 34 33 |
|
OneToOne | |
| cow (Bos Taurus) |
Mammalia | BEND3 34 33 |
|
OneToOne | |
| rat (Rattus norvegicus) |
Mammalia | Bend3 33 |
|
||
| mouse (Mus musculus) |
Mammalia | Bend3 16 34 33 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | BEND3 34 |
|
OneToOne | |
| chicken (Gallus gallus) |
Aves | BEND3 34 33 |
|
OneToOne | |
| lizard (Anolis carolinensis) |
Reptilia | BEND3 34 |
|
OneToOne | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | bend3 33 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | bend3 34 33 |
|
OneToOne |
- 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)
- Aminode:
- Evolutionary constrained regions (ECRs) for BEND3: view image
Paralogs for BEND3 Gene
Pseudogenes.org Pseudogenes for BEND3 Gene
No data available for Paralogs for BEND3 Gene
Variants 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 |
| 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 |
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
- A novel TPR-BEN domain interaction mediates PICH-BEND3 association. (PMID: 28977671) Pitchai GP … Hickson ID (Nucleic acids research 2017) 3 4 58
- 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
- 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
- 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
- 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
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- Invitrogen Antibodies for BEND3 (AFLGC-BEND3)
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- antibodies-online: Search results for available BEND3 related products ranked by validation data
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- GeneTex BEND3 Antibody for BEND3
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- Overview of 55 available BEND3 gene related products
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- Overview of 55 available BEND3 gene related products
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Sources for BEND3 Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) GO
- (12) TrEMBL
- (13) InterPro
- (14) ProtoNet
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) IntAct
- (22) Novoseek
- (23) PharmGKB
- (24) DrugBank
- (25) HMDB
- (26) UniGene
- (27) AceView
- (28) ASD
- (29) ECgene
- (30) GeneAnnot
- (31) CGAP SAGE
- (32) SOURCE
- (33) HomoloGene
- (34) PanEnsembl
- (35) euGenes
- (36) SGD
- (37) FlyBase
- (38) WormBase
- (39) Pseudogene
- (40) DGV
- (41) dbSNP
- (42) GenAtlas
- (43) HGMD
- (44) GAD
- (45) BGMUT
- (46) HuGE
- (47) Atlas
- (48) Cell Signaling Technology
- (49) GenBank
- (50) H-invDB
- (51) HORDE
- (52) HUGE
- (53) IMGT
- (54) Leiden
- (55) miRBase
- (56) DME
- (57) OriGene
- (58) PubMed
- (59) R&D Systems
- (60) TGDB
- (61) Tocris
- (62) Abcam
- (63) Novus Biologicals
- (64) ProSpec
- (65) Sino Biological
- (66) GenScript
- (67) Qiagen
- (68) Cloud-Clone Corp.
- (69) OCA
- (70) Proteopedia
- (71) MOPED
- (72) neXtProt
- (73) Reactome
- (74) GeneGo (Thomson Reuters)
- (75) fRNAdb
- (76) DISEASES
- (77) SIMAP
- (78) GenomeRNAi
- (79) LifeMap
- (80) miRTarBase
- (81) MalaCards
- (82) Invitrogen
- (83) BitterDB
- (84) Vector BioLabs
- (85) ESI-BIO
- (86) RefSeq
- (87) BioSystems
- (88) MaxQB
- (89) IUPHAR
- (90) BioGPS
- (91) Illumina
- (92) COMPARTMENTS
- (93) HOMER
- (94) PaxDb
- (95) ApexBio
- (96) Addgene
- (97) antibodies-online
- (98) CYP
- (99) NONCODE
- (100) SwitchGear Genomics
- (101) TreeFam
- (102) PathCards
- (103) GeneReviews
- (104) GeneTex
- (105) Taconic Biosciences
- (106) GTEx
- (107) ProteomicsDB
- (108) SCBT
- (109) DGIdb
- (110) ClinicalTrials
- (111) FDA Approved Drugs
- (112) RVIS
- (113) SIGNOR
- (114) diseasecard
- (115) NIH Rare Diseases
- (116) Orphanet
- (117) UMLS
- (118) GTR
- (119) Disease Ontology
- (120) Genetics Home Reference
- (121) MeSH
- (122) MedlinePlus
- (123) CDC
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