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Aliases for KLF9 Gene

Aliases for KLF9 Gene

  • Kruppel Like Factor 9 2 3 5
  • Basic Transcription Element-Binding Protein 1 3 4
  • Transcription Factor BTEB1 3 4
  • GC-Box-Binding Protein 1 3 4
  • BTE-Binding Protein 1 3 4
  • BTEB1 3 4
  • BTEB 3 4
  • Basic Transcription Element Binding Protein 1 2
  • Krueppel-Like Factor 9 3

External Ids for KLF9 Gene

Previous HGNC Symbols for KLF9 Gene

  • BTEB1

Previous GeneCards Identifiers for KLF9 Gene

  • GC09M070230
  • GC09M072189
  • GC09M072999
  • GC09M042839

Summaries for KLF9 Gene

Entrez Gene Summary for KLF9 Gene

  • The protein encoded by this gene is a transcription factor that binds to GC box elements located in the promoter. Binding of the encoded protein to a single GC box inhibits mRNA expression while binding to tandemly repeated GC box elements activates transcription. [provided by RefSeq, Jul 2008]

GeneCards Summary for KLF9 Gene

KLF9 (Kruppel Like Factor 9) is a Protein Coding gene. Diseases associated with KLF9 include Otosclerosis. Among its related pathways are Circadian rythm related genes and Diurnally Regulated Genes with Circadian Orthologs. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity. An important paralog of this gene is KLF13.

UniProtKB/Swiss-Prot for KLF9 Gene

  • Transcription factor that binds to GC box promoter elements. Selectively activates mRNA synthesis from genes containing tandem repeats of GC boxes but represses genes with a single GC box. Acts as an epidermal circadian transcription factor regulating keratinocyte proliferation (PubMed:22711835).

Gene Wiki entry for KLF9 Gene

Additional gene information for KLF9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KLF9 Gene

Genomics for KLF9 Gene

GeneHancer (GH) Regulatory Elements for KLF9 Gene

Promoters and enhancers for KLF9 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
GH09J070409 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 653.6 +2.2 2154 6.6 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARNT ZFP64 ARID4B SIN3A FEZF1 KLF9 SMC5 PTAR1 GC09P070383
GH09J070415 Enhancer 0.4 dbSUPER 650.7 -1.7 -1683 1 ZNF316 PRDM1 KLF9 LOC101927086
GH09J070483 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 15.5 -70.2 -70189 3.4 HDGF PKNOX1 SMAD1 ATF1 ARNT ARID4B NCOA2 TCF12 GATA2 ZNF143 KLF9 SMC5-AS1 LOC105376079 GC09P070531 LOC101927086
GH09J070599 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 12.8 -186.8 -186777 3.2 ATF1 FEZF1 IRF4 YY1 GLIS2 ARID2 ZNF143 FOS RUNX3 RXRA SMC5 PTAR1 KLF9 TRPM3 GC09P070607 RN7SL726P LOC101927086
GH09J070476 Enhancer 1.2 Ensembl ENCODE dbSUPER 15.7 -65.2 -65151 5.8 FOXA2 NFIB SIN3A RAD21 YY1 ZNF614 EGR1 FOS EGR2 RXRA KLF9 LOC105376079 GC09P070531 LOC101927086
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KLF9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the KLF9 gene promoter:
  • Sp1
  • E2F-3a
  • E2F
  • E2F-1
  • E2F-2
  • E2F-4
  • E2F-5
  • ARP-1
  • LCR-F1
  • CBF(2)

Genomic Locations for KLF9 Gene

Genomic Locations for KLF9 Gene
30,061 bases
Minus strand
30,071 bases
Minus strand

Genomic View for KLF9 Gene

Genes around KLF9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KLF9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KLF9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KLF9 Gene

Proteins for KLF9 Gene

  • Protein details for KLF9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Krueppel-like factor 9
    Protein Accession:
    Secondary Accessions:
    • B2R943
    • Q16196

    Protein attributes for KLF9 Gene

    244 amino acids
    Molecular mass:
    27235 Da
    Quaternary structure:
    No Data Available

neXtProt entry for KLF9 Gene

Post-translational modifications for KLF9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for KLF9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for KLF9 Gene

Domains & Families for KLF9 Gene

Gene Families for KLF9 Gene

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

Protein Domains for KLF9 Gene

Suggested Antigen Peptide Sequences for KLF9 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Sp1 C2H2-type zinc-finger protein family.
  • Belongs to the Sp1 C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with KLF9: view

Function for KLF9 Gene

Molecular function for KLF9 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor that binds to GC box promoter elements. Selectively activates mRNA synthesis from genes containing tandem repeats of GC boxes but represses genes with a single GC box. Acts as an epidermal circadian transcription factor regulating keratinocyte proliferation (PubMed:22711835).
UniProtKB/Swiss-Prot Induction:
Expression is highly sensitive to glucocorticoids and shows diurnal expression patterns. A strong induction of expression seen during keratinocyte differentiation in a cortisol dependent manner.

Phenotypes From GWAS Catalog for KLF9 Gene

Gene Ontology (GO) - Molecular Function for KLF9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity TAS 1356762
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with KLF9: view
genes like me logo Genes that share phenotypes with KLF9: view

Animal Models for KLF9 Gene

MGI Knock Outs for KLF9:
  • Klf9 Klf9<tm1.1(KOMP)Vlcg>
  • Klf9 Klf9<tm1Yfk>

Animal Model Products

Targeted motifs for KLF9 Gene
HOMER Transcription Factor Regulatory Elements motif KLF9
  • Consensus sequence: GCCACRCCCACY Submotif: canonical Cell Type: GBM GEO ID: GSE62211

Clone Products

  • Addgene plasmids for KLF9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for KLF9 Gene

Localization for KLF9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for KLF9 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 KLF9 gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for KLF9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 22711835
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with KLF9: view

Pathways & Interactions for KLF9 Gene

genes like me logo Genes that share pathways with KLF9: view

Pathways by source for KLF9 Gene

Gene Ontology (GO) - Biological Process for KLF9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II TAS 1356762
GO:0007623 circadian rhythm IEP 22711835
GO:0010839 negative regulation of keratinocyte proliferation IMP 22711835
genes like me logo Genes that share ontologies with KLF9: view

No data available for SIGNOR curated interactions for KLF9 Gene

Drugs & Compounds for KLF9 Gene

(3) Drugs for KLF9 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with KLF9: view

Transcripts for KLF9 Gene

mRNA/cDNA for KLF9 Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(312) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for KLF9 Gene

Kruppel-like factor 9:
Representative Sequences:

Clone Products

  • Addgene plasmids for KLF9

Alternative Splicing Database (ASD) splice patterns (SP) for KLF9 Gene

No ASD Table

Relevant External Links for KLF9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for KLF9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KLF9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of KLF9 Gene:


SOURCE GeneReport for Unigene cluster for KLF9 Gene:


mRNA Expression by UniProt/SwissProt for KLF9 Gene:

Tissue specificity: Epidermis (at protein level).

Evidence on tissue expression from TISSUES for KLF9 Gene

  • Liver(4.5)
  • Lung(4.5)
  • Nervous system(3)
  • Thyroid gland(2.8)
  • Kidney(2.2)
genes like me logo Genes that share expression patterns with KLF9: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for KLF9 Gene

Orthologs for KLF9 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for KLF9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia KLF9 34 33
  • 99.45 (n)
(Canis familiaris)
Mammalia KLF9 34
  • 98 (a)
(Bos Taurus)
Mammalia KLF9 34 33
  • 96.86 (n)
(Rattus norvegicus)
Mammalia Klf9 33
  • 94.95 (n)
(Mus musculus)
Mammalia Klf9 16 34 33
  • 94.13 (n)
(Monodelphis domestica)
Mammalia KLF9 34
  • 92 (a)
(Ornithorhynchus anatinus)
Mammalia KLF9 34
  • 88 (a)
(Gallus gallus)
Aves KLF9 34 33
  • 74.17 (n)
(Anolis carolinensis)
Reptilia KLF9 34
  • 60 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia klf9 33
  • 71.94 (n)
African clawed frog
(Xenopus laevis)
Amphibia bteb1-A 33
(Danio rerio)
Actinopterygii klf9 34
  • 47 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1235 33
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7373 34
  • 14 (a)
Species where no ortholog for KLF9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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 KLF9 Gene

Gene Tree for KLF9 (if available)
Gene Tree for KLF9 (if available)
Evolutionary constrained regions (ECRs) for KLF9: view image

Paralogs for KLF9 Gene

Paralogs for KLF9 Gene

(32) SIMAP similar genes for KLF9 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with KLF9: view

Variants for KLF9 Gene

Sequence variations from dbSNP and Humsavar for KLF9 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000023143 -- 70,386,642(-) T/C 3_prime_UTR_variant
rs1000048041 -- 70,393,893(-) T/C intron_variant
rs1000152466 -- 70,393,507(-) C/A/T intron_variant
rs1000266109 -- 70,400,472(-) G/A intron_variant
rs1000312031 -- 70,387,163(-) G/A 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for KLF9 Gene

Variant ID Type Subtype PubMed ID
esv1491500 CNV insertion 17803354
nsv1047862 CNV gain 25217958
nsv1049132 CNV gain 25217958
nsv428219 CNV loss 18775914
nsv831615 CNV gain 17160897

Variation tolerance for KLF9 Gene

Residual Variation Intolerance Score: 50.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.19; 23.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KLF9 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 KLF9 Gene

Disorders for KLF9 Gene

MalaCards: The human disease database

(1) MalaCards diseases for KLF9 Gene - From: GeneCards

Disorder Aliases PubMed IDs
- elite association - COSMIC cancer census association via MalaCards
Search KLF9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for KLF9

genes like me logo Genes that share disorders with KLF9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for KLF9 Gene

Publications for KLF9 Gene

  1. Cell-specific translational control of transcription factor BTEB expression. The role of an upstream AUG in the 5'-untranslated region. (PMID: 8051167) Imataka H … Hayami M (The Journal of biological chemistry 1994) 3 4 22 58
  2. Two regulatory proteins that bind to the basic transcription element (BTE), a GC box sequence in the promoter region of the rat P-4501A1 gene. (PMID: 1356762) Imataka H … Fujii-Kuriyama Y (The EMBO journal 1992) 2 3 22 58
  3. Krüppel-like factor 9 is a circadian transcription factor in human epidermis that controls proliferation of keratinocytes. (PMID: 22711835) Spörl F … Kramer A (Proceedings of the National Academy of Sciences of the United States of America 2012) 3 4 58
  4. Kruppel-like factor 9 is a negative regulator of ligand-dependent estrogen receptor alpha signaling in Ishikawa endometrial adenocarcinoma cells. (PMID: 17717078) Velarde MC … Simmen RC (Molecular endocrinology (Baltimore, Md.) 2007) 3 22 58
  5. Progesterone receptor transactivation of the secretory leukocyte protease inhibitor gene in Ishikawa endometrial epithelial cells involves recruitment of Krüppel-like factor 9/basic transcription element binding protein-1. (PMID: 16384861) Velarde MC … Simmen RC (Endocrinology 2006) 3 22 58

Products for KLF9 Gene

Sources for KLF9 Gene

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