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Aliases for ZBED9 Gene

Aliases for ZBED9 Gene

  • Zinc Finger BED-Type Containing 9 2 3 5
  • Transposon-Derived Buster4 Transposase-Like Protein 3 4
  • Zinc Finger BED Domain-Containing Protein 9 3 4
  • Zinc Finger Protein 305 Pseudogene 2 2 3
  • SCAN Domain Containing 3 2 3
  • Zinc Finger Protein 452 2 3
  • ZNF305P2 3 4
  • Buster4 3 4
  • SCAND3 3 4
  • ZNF452 3 4
  • SCAN Domain-Containing Protein 3 3
  • DJ1186N24.3 3
  • KIAA1925 4
  • ZFP38-L 3

External Ids for ZBED9 Gene

Previous HGNC Symbols for ZBED9 Gene

  • ZNF305P2
  • ZNF452
  • SCAND3

Summaries for ZBED9 Gene

GeneCards Summary for ZBED9 Gene

ZBED9 (Zinc Finger BED-Type Containing 9) 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 ZBED5.

Gene Wiki entry for ZBED9 Gene

Additional gene information for ZBED9 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZBED9 Gene

Genomics for ZBED9 Gene

GeneHancer (GH) Regulatory Elements for ZBED9 Gene

Promoters and enhancers for ZBED9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J028586 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.3 +29.0 29047 1.9 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 ZNF143 SP3 TRQ-TTG2-1 ZBED9 GPX6 GPX5 ZKSCAN3 ZNF311 ZNF603P ZSCAN12 ZNF90P2 KRT18P1
GH06J028615 Enhancer 1 ENCODE 656.4 -0.1 -88 0.8 SMAD1 ATF1 ARNT POLR2B ZNF766 CBX5 GATA2 E2F8 ZFP91 ATF7 ZBED9 GC06M028606 ZKSCAN4 ZKSCAN3 ZSCAN9 ZSCAN12 ZKSCAN8 ZNF311 GPX6 TRIM27
GH06J028647 Promoter/Enhancer 1.5 Ensembl ENCODE 6.5 -32.5 -32470 1.9 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF213 E2F8 TRT-CGT3-1 LINC00533 GC06M028665 ZKSCAN8 ZSCAN12 ZKSCAN3 ZSCAN23 ZKSCAN4 GPX5 SUMO2P1
GH06J028673 Enhancer 1.1 Ensembl ENCODE 5.1 -58.0 -58036 1.1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 GTF3C2 FOS SP3 TRA-CGC2-1 GC06M028676 ZSCAN12 ZSCAN23 ZKSCAN8 ZKSCAN3 PGBD1 ZSCAN26 ZNF603P ZKSCAN4
GH06J028553 Enhancer 1.2 Ensembl ENCODE 4.6 +62.2 62201 1.5 HDGF PKNOX1 ARNT YBX1 YY1 POLR2B ZNF766 E2F8 ZHX2 MXD4 ZKSCAN4 ZNF603P ZKSCAN3 ZSCAN9 ZSCAN12 ZKSCAN8 ZSCAN23 GPX5 ZNF311 OR2E1P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZBED9 on UCSC Golden Path with GeneCards custom track

Genomic Locations for ZBED9 Gene

Genomic Locations for ZBED9 Gene
45,678 bases
Minus strand
44,583 bases
Minus strand

Genomic View for ZBED9 Gene

Genes around ZBED9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZBED9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZBED9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZBED9 Gene

Proteins for ZBED9 Gene

  • Protein details for ZBED9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    SCAN domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • Q2NKL9
    • Q5SRJ3
    • Q8TCN2
    • Q96MV9
    • Q96PW3

    Protein attributes for ZBED9 Gene

    1325 amino acids
    Molecular mass:
    151666 Da
    Quaternary structure:
    No Data Available

neXtProt entry for ZBED9 Gene

Post-translational modifications for ZBED9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ZBED9 Gene

No data available for DME Specific Peptides for ZBED9 Gene

Domains & Families for ZBED9 Gene

Gene Families for ZBED9 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for ZBED9 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ZBED9: view

No data available for UniProtKB/Swiss-Prot for ZBED9 Gene

Function for ZBED9 Gene

Phenotypes From GWAS Catalog for ZBED9 Gene

Gene Ontology (GO) - Molecular Function for ZBED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IBA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IBA --
GO:0003700 DNA binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with ZBED9: view
genes like me logo Genes that share phenotypes with ZBED9: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZBED9

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZBED9 Gene

Localization for ZBED9 Gene

Subcellular locations from

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 ZBED9 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZBED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IBA --
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with ZBED9: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for ZBED9 Gene

Pathways & Interactions for ZBED9 Gene

SuperPathways for ZBED9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZBED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0015074 DNA integration IEA --
genes like me logo Genes that share ontologies with ZBED9: view

No data available for Pathways by source and SIGNOR curated interactions for ZBED9 Gene

Drugs & Compounds for ZBED9 Gene

No Compound Related Data Available

Transcripts for ZBED9 Gene

mRNA/cDNA for ZBED9 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZBED9

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZBED9 Gene

No ASD Table

Relevant External Links for ZBED9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZBED9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZBED9 Gene

Protein differential expression in normal tissues from HIPED for ZBED9 Gene

This gene is overexpressed in Lung (45.5) and Placenta (23.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ZBED9 Gene

Protein tissue co-expression partners for ZBED9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZBED9 Gene:


Evidence on tissue expression from TISSUES for ZBED9 Gene

  • Eye(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with ZBED9: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZBED9 Gene

Orthologs for ZBED9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ZBED9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SCAND3 34 33
  • 99.57 (n)
(Canis familiaris)
Mammalia SCAND3 34 33
  • 86.26 (n)
(Mus musculus)
Mammalia 2410018M08Rik 34
  • 32 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 32 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101733657 33
  • 51.36 (n)
(Danio rerio)
Actinopterygii BX664605.1 34
  • 34 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 27 (a)
Species where no ortholog for ZBED9 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • 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)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for ZBED9 Gene

Gene Tree for ZBED9 (if available)
Gene Tree for ZBED9 (if available)
Evolutionary constrained regions (ECRs) for ZBED9: view image

Paralogs for ZBED9 Gene

genes like me logo Genes that share paralogs with ZBED9: view

Variants for ZBED9 Gene

Sequence variations from dbSNP and Humsavar for ZBED9 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000132932 -- 28,616,829(-) G/C upstream_transcript_variant
rs1000145115 -- 28,598,450(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000316884 -- 28,589,642(-) A/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000439885 -- 28,598,890(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000480560 -- 28,605,047(-) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ZBED9 Gene

Variant ID Type Subtype PubMed ID
dgv3296n106 CNV deletion 24896259
esv3576110 CNV gain 25503493
esv3608457 CNV gain 21293372
esv3608458 CNV gain 21293372
nsv1074388 CNV deletion 25765185
nsv601210 CNV gain 21841781
nsv830621 CNV gain 17160897

Variation tolerance for ZBED9 Gene

Residual Variation Intolerance Score: 27.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.90; 59.23% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZBED9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZBED9 Gene

Disorders for ZBED9 Gene

Additional Disease Information for ZBED9

No disorders were found for ZBED9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZBED9 Gene

Publications for ZBED9 Gene

  1. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. (PMID: 23533661) Hayward A … Jern P (PloS one 2013) 2 3 4 58
  2. On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain. (PMID: 23550032) Llorens C … Moya A (Mobile genetic elements 2012) 2 3 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4 58

Products for ZBED9 Gene

Sources for ZBED9 Gene

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