ZBED6 Gene (Protein Coding)

Zinc Finger BED-Type Containing 6

GC01P203796
GIFtS:
30
The protein encoded by this transposon-derived intronless gene is a transcriptional repressor that binds to the consensus sequence 5'-GCTCGC-3'. The encoded protein has been shown to repress IGF2 transcription. This gene is located within the first intron of the ZC3H11A gene. [provided by RefSeq, Jul 2016] See more...

Aliases for ZBED6 Gene

Aliases for ZBED6 Gene

  • Zinc Finger BED-Type Containing 6 2 3 5
  • Zinc Finger BED Domain-Containing Protein 6 3 4
  • MGR 3

External Ids for ZBED6 Gene

Previous GeneCards Identifiers for ZBED6 Gene

  • GC01U902782
  • GC01P203766

Summaries for ZBED6 Gene

Entrez Gene Summary for ZBED6 Gene

  • The protein encoded by this transposon-derived intronless gene is a transcriptional repressor that binds to the consensus sequence 5'-GCTCGC-3'. The encoded protein has been shown to repress IGF2 transcription. This gene is located within the first intron of the ZC3H11A gene. [provided by RefSeq, Jul 2016]

GeneCards Summary for ZBED6 Gene

ZBED6 (Zinc Finger BED-Type Containing 6) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and protein dimerization activity. An important paralog of this gene is ZBED4.

UniProtKB/Swiss-Prot Summary for ZBED6 Gene

  • Transcriptional repressor which binds to the consensus sequence 5'-GCTCGC-3' and represses transcription of IGF2. May also regulate expression of other target genes containing this consensus binding site (By similarity).

Additional gene information for ZBED6 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ZBED6 Gene

Genomics for ZBED6 Gene

GeneHancer (GH) Regulatory Elements for ZBED6 Gene

Promoters and enhancers for ZBED6 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
GH01J203793 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 761.9 +0.4 393 4.2 SIN3A ZBTB40 SREBF1 SIX5 ZBTB6 MLX SMARCE1 RBPJ POLR2A USF2 ZC3H11A ZBED6 lnc-ZC3H11A-1 MDM4 SNRPE KDM5B LAX1 PPP1R15B HNRNPA1P59 ENSG00000240219
GH01J203801 Promoter 0.3 EPDnew 750.4 +6.1 6100 0.1 lnc-ETNK2-7 ZBED6 SNRPE LOC100420338 ZC3H11A lnc-ZC3H11A-1
GH01J203802 Promoter 0.3 EPDnew 750.4 +6.8 6810 0.1 lnc-ETNK2-7 ZBED6 LAX1 SNRPE LOC100420338 ZC3H11A
GH01J203817 Promoter 0.3 EPDnew 750.3 +21.4 21393 0.1 ZBED6 SNRPE SNORA77 LAX1 OPTC ETNK2 ENSG00000231691 PLEKHA6 ENSG00000227417 ENSG00000223505
GH01J203848 Promoter 0.3 EPDnew 750.2 +52.6 52597 0.1 ZBED6 piR-30400-001 RPL35AP5 ZC3H11A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZBED6 on UCSC Golden Path with GeneCards custom track

Genomic Locations for ZBED6 Gene

Genomic Locations for ZBED6 Gene
chr1:203,795,714-203,854,999
(GRCh38/hg38)
Size:
59,286 bases
Orientation:
Plus strand
chr1:203,765,437-203,769,686
(GRCh37/hg19)
Size:
4,250 bases
Orientation:
Plus strand

Genomic View for ZBED6 Gene

Genes around ZBED6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZBED6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZBED6 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for ZBED6 Gene

Proteins for ZBED6 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for ZBED6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P86452-ZBED6_HUMAN
    Recommended name:
    Zinc finger BED domain-containing protein 6
    Protein Accession:
    P86452

    Protein attributes for ZBED6 Gene

    Size:
    979 amino acids
    Molecular mass:
    109973 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Encoded by an exapted DNA transposon located in an intron of the ZC3H11A gene.

neXtProt entry for ZBED6 Gene

Protein Expression for ZBED6 Gene

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

Post-translational modifications for ZBED6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ZBED6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZBED6 Gene

Domains & Families for ZBED6 Gene

Gene Families for ZBED6 Gene

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

Protein Domains for ZBED6 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ZBED6 Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger BED domain-containing protein 6 (ZBED6_HUMAN)
genes like me logo Genes that share domains with ZBED6: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for ZBED6 Gene

Function for ZBED6 Gene

Products:

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

Molecular function for ZBED6 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor which binds to the consensus sequence 5'-GCTCGC-3' and represses transcription of IGF2. May also regulate expression of other target genes containing this consensus binding site (By similarity).

Phenotypes From GWAS Catalog for ZBED6 Gene

Gene Ontology (GO) - Molecular Function for ZBED6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0003677 DNA binding IEA --
GO:0046872 metal ion binding IEA --
GO:0046983 protein dimerization activity IEA --
genes like me logo Genes that share ontologies with ZBED6: view
genes like me logo Genes that share phenotypes with ZBED6: view

Animal Models for ZBED6 Gene

MGI Knock Outs for ZBED6:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZBED6

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ZBED6 Gene

Localization for ZBED6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZBED6 Gene

Nucleus. Nucleus, nucleolus. Note=Located predominantly in the nucleolus but is also dispersed throughout the nucleus. {ECO:0000250 UniProtKB:D2EAC2}.

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 ZBED6 gene
Compartment Confidence
nucleus 4

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for ZBED6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005730 nucleolus ISS --
genes like me logo Genes that share ontologies with ZBED6: view

Pathways & Interactions for ZBED6 Gene

PathCards logo

SuperPathways for ZBED6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZBED6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0045892 negative regulation of transcription, DNA-templated ISS --
genes like me logo Genes that share ontologies with ZBED6: view

No data available for Pathways by source and SIGNOR curated interactions for ZBED6 Gene

Drugs & Compounds for ZBED6 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for ZBED6 Gene

Products:

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

mRNA/cDNA for ZBED6 Gene

(1) REFSEQ mRNAs :
(2) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZBED6

Alternative Splicing Database (ASD) splice patterns (SP) for ZBED6 Gene

No ASD Table

Relevant External Links for ZBED6 Gene

GeneLoc Exon Structure for
ZBED6
ECgene alternative splicing isoforms for
ZBED6

Expression for ZBED6 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZBED6 Gene

mRNA expression in normal human tissues for ZBED6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ZBED6 Gene

This gene is overexpressed in Islet of Langerhans (64.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ZBED6 Gene



Protein tissue co-expression partners for ZBED6 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZBED6 Gene:

ZBED6

SOURCE GeneReport for Unigene cluster for ZBED6 Gene:

Hs.716666
genes like me logo Genes that share expression patterns with ZBED6: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZBED6 Gene

Orthologs for ZBED6 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZBED6 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
 Mammalia ZBED6 33 32
  • 91.73 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia ZBED6 33 32
  • 91.1 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Zbed6 17 33 32
  • 89.49 (n)
lizard
(Anolis carolinensis)
 Reptilia ZBED6 33
  • 22 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia LOC101730718 32
  • 48.93 (n)
zebrafish
(Danio rerio)
 Actinopterygii BX530070.1 33
  • 21 (a)
 ManyToMany
fruit fly
(Drosophila melanogaster)
 Insecta CG13775 33
  • 18 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea C10A4.1 33
  • 18 (a)
 ManyToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 33
  • 23 (a)
 OneToMany
Species where no ortholog for ZBED6 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)
  • chicken (Gallus gallus)
  • chimpanzee (Pan troglodytes)
  • 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)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ZBED6 Gene

ENSEMBL:
Gene Tree for ZBED6 (if available)
TreeFam:
Gene Tree for ZBED6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ZBED6: view image

Paralogs for ZBED6 Gene

Paralogs for ZBED6 Gene

genes like me logo Genes that share paralogs with ZBED6: view

Variants for ZBED6 Gene

Sequence variations from dbSNP and Humsavar for ZBED6 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000870924 -- 203,801,526(+) G/A downstream_transcript_variant
rs1001048837 -- 203,795,692(+) G/A upstream_transcript_variant
rs1001557029 -- 203,799,448(+) G/A coding_sequence_variant, synonymous_variant
rs1001562186 -- 203,798,487(+) A/G coding_sequence_variant, missense_variant
rs1002778423 -- 203,800,695(+) G/A/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for ZBED6 Gene

Variant ID Type Subtype PubMed ID
nsv520482 CNV loss 19592680

Variation tolerance for ZBED6 Gene

Gene Damage Index Score: 11.79; 93.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZBED6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZBED6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZBED6 Gene

Disorders for ZBED6 Gene

Additional Disease Information for ZBED6

ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for ZBED6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZBED6 Gene

Publications for ZBED6 Gene

  1. ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. (PMID: 20016685) Markljung E … Andersson L (PLoS biology 2009) 2 3 4 56
  2. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. (PMID: 23533661) Hayward A … Jern P (PloS one 2013) 2 3 56
  3. Studying phenotypic evolution in domestic animals: a walk in the footsteps of Charles Darwin. (PMID: 20375320) Andersson L (Cold Spring Harbor symposia on quantitative biology 2009) 2 3 56
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 56
  5. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3 56

ExternalLinks

View latest publications for ZBED6 gene in Mastermind

Products for ZBED6 Gene

Sources for ZBED6 Gene