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Aliases for KRT39 Gene

Aliases for KRT39 Gene

  • Keratin 39 2 3 5
  • Keratin 39, Type I 2 3
  • Cytokeratin-39 3 4
  • CK-39 3 4
  • KA35 3 4
  • K39 3 4
  • Keratin, Type I Cytoskeletal 39 3
  • Type I Hair Keratin KA35 3
  • Type I Hair Keratin Ka35 4
  • Keratin-39 4

External Ids for KRT39 Gene

Previous GeneCards Identifiers for KRT39 Gene

  • GC17M036369
  • GC17M039114
  • GC17M034909

Summaries for KRT39 Gene

Entrez Gene Summary for KRT39 Gene

  • This gene encodes a member of the type I (acidic) keratin family, which belongs to the superfamily of intermediate filament (IF) proteins. Keratins are heteropolymeric structural proteins which form the intermediate filament. These filaments, along with actin microfilaments and microtubules, compose the cytoskeleton of epithelial cells. The type I keratin genes are clustered in a region of chromosome 17q12-q21. [provided by RefSeq, Jul 2009]

GeneCards Summary for KRT39 Gene

KRT39 (Keratin 39) is a Protein Coding gene. Among its related pathways are Keratinization and Developmental Biology. Gene Ontology (GO) annotations related to this gene include structural molecule activity. An important paralog of this gene is KRT36.

UniProtKB/Swiss-Prot for KRT39 Gene

  • May play a role in late hair differentiation.

Additional gene information for KRT39 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KRT39 Gene

Genomics for KRT39 Gene

GeneHancer (GH) Regulatory Elements for KRT39 Gene

Promoters and enhancers for KRT39 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
GH17I040966 Promoter 0.5 EPDnew 550.8 -0.1 -76 0.1 KRT39 KRT40 ENSG00000234477
GH17I040948 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.4 +12.2 12179 11.7 PKNOX1 FOXA2 MLX ZFP64 ARID4B NEUROD1 DMAP1 ZNF48 ETS1 TCF12 KRTAP3-2 KRT23 KRTAP2-1 KRT39 KRT40 KRTAP2-2 ENSG00000234477 KRTAP3-3 KRTAP1-5 KRTAP3-1
GH17I040935 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 6 +29.4 29406 3.6 SOX13 FOXA2 SAP130 ARID4B CEBPG ZNF48 GATA3 POLR2A SOX5 RFX1 KRT23 TMEM99 KRT39 KRTAP3-2 KRTAP2-1 GC17M040929 ENSG00000234477
GH17I040980 Enhancer 0.6 Ensembl ENCODE 12.8 -13.9 -13876 1.2 POLR2A MAFK KRT39 KRT40
GH17I040963 Enhancer 0.5 dbSUPER 0.8 +2.8 2823 1.5 CTCF IRF2 GATA3 ZNF189 SMC3 HOMEZ RAD21 KRT23 KRT40 KRTAP3-2 KRTAP2-1 KRTAP2-2 KRTAP3-3 ENSG00000234477 KRTAP1-5 KRTAP2-3 KRTAP4-6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around KRT39 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the KRT39 gene promoter:

Genomic Locations for KRT39 Gene

Genomic Locations for KRT39 Gene
8,476 bases
Minus strand

Genomic View for KRT39 Gene

Genes around KRT39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KRT39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KRT39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KRT39 Gene

Proteins for KRT39 Gene

  • Protein details for KRT39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Keratin, type I cytoskeletal 39
    Protein Accession:
    Secondary Accessions:
    • B2RXK6
    • Q6IFU6

    Protein attributes for KRT39 Gene

    491 amino acids
    Molecular mass:
    55651 Da
    Quaternary structure:
    • Heterotetramer of two type I and two type II keratins.
    • There are two types of cytoskeletal and microfibrillar keratin, I (acidic) and II (neutral to basic) (40-55 and 56-70 kDa, respectively).

neXtProt entry for KRT39 Gene

Post-translational modifications for KRT39 Gene

No Post-translational modifications

Other Protein References for KRT39 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for KRT39 Gene

Domains & Families for KRT39 Gene

Gene Families for KRT39 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for KRT39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the intermediate filament family.
  • Belongs to the intermediate filament family.
genes like me logo Genes that share domains with KRT39: view

Function for KRT39 Gene

Molecular function for KRT39 Gene

UniProtKB/Swiss-Prot Function:
May play a role in late hair differentiation.

Gene Ontology (GO) - Molecular Function for KRT39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IEA --
genes like me logo Genes that share ontologies with KRT39: view
genes like me logo Genes that share phenotypes with KRT39: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for KRT39 Gene

Localization for KRT39 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 KRT39 gene
Compartment Confidence
cytosol 5
cytoskeleton 3
nucleus 2
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for KRT39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0005882 intermediate filament IEA --
genes like me logo Genes that share ontologies with KRT39: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for KRT39 Gene

Pathways & Interactions for KRT39 Gene

SuperPathways for KRT39 Gene

SuperPathway Contained pathways
1 Developmental Biology
2 Keratinization
genes like me logo Genes that share pathways with KRT39: view

Pathways by source for KRT39 Gene

2 Reactome pathways for KRT39 Gene

Interacting Proteins for KRT39 Gene

Gene Ontology (GO) - Biological Process for KRT39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031424 keratinization TAS --
GO:0070268 cornification TAS --
genes like me logo Genes that share ontologies with KRT39: view

No data available for SIGNOR curated interactions for KRT39 Gene

Drugs & Compounds for KRT39 Gene

No Compound Related Data Available

Transcripts for KRT39 Gene

mRNA/cDNA for KRT39 Gene

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

Unigene Clusters for KRT39 Gene

Keratin 39:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for KRT39 Gene

No ASD Table

Relevant External Links for KRT39 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for KRT39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KRT39 Gene

mRNA differential expression in normal tissues according to GTEx for KRT39 Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x42.2) and Skin - Sun Exposed (Lower leg) (x6.2).

Protein differential expression in normal tissues from HIPED for KRT39 Gene

This gene is overexpressed in Hair follicle (68.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for KRT39 Gene

Protein tissue co-expression partners for KRT39 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of KRT39 Gene:


SOURCE GeneReport for Unigene cluster for KRT39 Gene:


mRNA Expression by UniProt/SwissProt for KRT39 Gene:

Tissue specificity: Expressed in skin and scalp. In the hair follicle, it is present in the upper hair cuticle and the upper cortex. Also present in the in the upper portion of beard hairs (at protein level).

Evidence on tissue expression from TISSUES for KRT39 Gene

  • Skin(4.2)
genes like me logo Genes that share expression patterns with KRT39: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for KRT39 Gene

Orthologs for KRT39 Gene

This gene was present in the common ancestor of chordates.

Orthologs for KRT39 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia KRT39 33 34
  • 99.19 (n)
(Canis familiaris)
Mammalia KRT39 33 34
  • 83.51 (n)
(Bos Taurus)
Mammalia KRT39 33 34
  • 83.23 (n)
(Rattus norvegicus)
Mammalia Krt39 33
  • 79.9 (n)
(Mus musculus)
Mammalia Krt39 33 16 34
  • 79.86 (n)
(Monodelphis domestica)
Mammalia KRT39 34
  • 57 (a)
(Ornithorhynchus anatinus)
Mammalia KRT39 34
  • 56 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 49 (a)
-- 34
  • 40 (a)
(Danio rerio)
Actinopterygii cyt1 34
  • 38 (a)
cyt1l 34
  • 38 (a)
zgc:109868 34
  • 38 (a)
krt17 34
  • 37 (a)
wu:fb17f05 34
  • 37 (a)
zgc:92061 34
  • 37 (a)
krt1-19d 34
  • 35 (a)
zgc:153629 34
  • 35 (a)
zgc:136902 34
  • 34 (a)
zgc:92035 34
  • 34 (a)
krt15 34
  • 33 (a)
si:dkeyp-113d7.4 34
  • 32 (a)
BX469912.1 34
  • 19 (a)
zgc:92533 34
  • 19 (a)
Species where no ortholog for KRT39 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)
  • 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)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for KRT39 Gene

Gene Tree for KRT39 (if available)
Gene Tree for KRT39 (if available)

Paralogs for KRT39 Gene

genes like me logo Genes that share paralogs with KRT39: view

Variants for KRT39 Gene

Sequence variations from dbSNP and Humsavar for KRT39 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs483352776 uncertain-significance, not provided 40,958,616(-) T/G coding_sequence_variant, missense_variant
rs1000154345 -- 40,960,816(-) TT/ intron_variant
rs1001415640 -- 40,965,501(-) C/T intron_variant
rs1002052016 -- 40,968,029(-) T/A upstream_transcript_variant
rs1002343409 -- 40,961,384(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for KRT39 Gene

Variant ID Type Subtype PubMed ID
nsv9550 CNV loss 18304495
nsv574999 CNV loss 21841781
nsv1146669 OTHER inversion 26484159
esv3640560 CNV gain 21293372
esv3640559 CNV gain 21293372
esv2761957 CNV gain 21179565

Variation tolerance for KRT39 Gene

Residual Variation Intolerance Score: 84.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.62; 86.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KRT39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KRT39 Gene

Disorders for KRT39 Gene

Additional Disease Information for KRT39

No disorders were found for KRT39 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for KRT39 Gene

Publications for KRT39 Gene

  1. Novel type I hair keratins K39 and K40 are the last to be expressed in differentiation of the hair: completion of the human hair keratin catalog. (PMID: 17301834) Langbein L … Schweizer J (The Journal of investigative dermatology 2007) 3 4 58
  2. New consensus nomenclature for mammalian keratins. (PMID: 16831889) Schweizer J … Wright MW (The Journal of cell biology 2006) 2 3 58
  3. Comprehensive analysis of keratin gene clusters in humans and rodents. (PMID: 15085952) Hesse M … Magin TM (European journal of cell biology 2004) 3 4 58
  4. The human type I keratin gene family: characterization of new hair follicle specific members and evaluation of the chromosome 17q21.2 gene domain. (PMID: 15617563) Rogers MA … Schweizer J (Differentiation; research in biological diversity 2004) 3 4 58
  5. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PMID: 16625196) Zody MC … Nusbaum C (Nature 2006) 4 58

Products for KRT39 Gene

Sources for KRT39 Gene

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