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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 Developmental Biology. 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.

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

Genomics for KRT39 Gene

Regulatory Elements for KRT39 Gene

Enhancers for KRT39 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17F040980 1 Ensembl ENCODE 12.7 -13.9 -13876 1.2 POLR2A MAFK KRT39 KRT40
GH17F040948 1.1 FANTOM5 Ensembl ENCODE 11.3 +12.2 12179 11.7 PKNOX1 ATF1 MLX ZFP64 ARID4B DMAP1 ZNF48 SLC30A9 ZNF121 ZNF143 KRTAP3-2 KRT23 KRTAP2-1 KRT39 KRT40 KRTAP2-2 ENSG00000234477 KRTAP3-3 KRTAP1-5 KRTAP3-1
GH17F040935 1 FANTOM5 Ensembl ENCODE 6 +29.4 29406 3.6 SOX13 CTCF TBP SAP130 ARID4B CEBPG ZNF48 RAD21 RARA GATA3 KRT23 TMEM99 KRT39 KRTAP3-2 KRTAP2-1 GC17M040929
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around KRT39 on UCSC Golden Path with GeneCards custom track

Genomic Location for KRT39 Gene

40,958,417 bp from pter
40,966,892 bp from pter
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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

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

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

Localization for KRT39 Gene

Subcellular locations from

Jensen Localization Image for KRT39 Gene COMPARTMENTS Subcellular localization image for KRT39 gene
Compartment Confidence
cytoskeleton 3
cytosol 3
nucleus 2
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for KRT39 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 for KRT39 Gene

Pathways & Interactions for KRT39 Gene

SuperPathways for KRT39 Gene

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

Pathways by source for KRT39 Gene

1 Reactome pathway for KRT39 Gene

Interacting Proteins for KRT39 Gene

Selected Interacting proteins: Q6A163-K1C39_HUMAN for KRT39 Gene via IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for KRT39 Gene


No data available for SIGNOR curated interactions for KRT39 Gene

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:

Inhibitory RNA Products

Clone Products

Flow Cytometry 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 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).
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 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 34 35
  • 99.19 (n)
(Canis familiaris)
Mammalia KRT39 34 35
  • 83.51 (n)
(Bos Taurus)
Mammalia KRT39 34 35
  • 83.23 (n)
(Rattus norvegicus)
Mammalia Krt39 34
  • 79.9 (n)
(Mus musculus)
Mammalia Krt39 34 16 35
  • 79.86 (n)
(Monodelphis domestica)
Mammalia KRT39 35
  • 57 (a)
(Ornithorhynchus anatinus)
Mammalia KRT39 35
  • 56 (a)
(Anolis carolinensis)
Reptilia -- 35
  • 49 (a)
-- 35
  • 40 (a)
(Danio rerio)
Actinopterygii cyt1 35
  • 38 (a)
cyt1l 35
  • 38 (a)
zgc:109868 35
  • 38 (a)
krt17 35
  • 37 (a)
wu:fb17f05 35
  • 37 (a)
zgc:92061 35
  • 37 (a)
krt1-19d 35
  • 35 (a)
zgc:153629 35
  • 35 (a)
zgc:136902 35
  • 34 (a)
zgc:92035 35
  • 34 (a)
krt15 35
  • 33 (a)
si:dkeyp-113d7.4 35
  • 32 (a)
BX469912.1 35
  • 19 (a)
zgc:92533 35
  • 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

Variants for KRT39 Gene

Sequence variations from dbSNP and Humsavar for KRT39 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs17843021 --
rs17843023 --
rs7213256 --

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

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

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)

Relevant External Links 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

Relevant External Links for KRT39

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

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. (J. Invest. Dermatol. 2007) 3 4 64
  2. New consensus nomenclature for mammalian keratins. (PMID: 16831889) Schweizer J. … Wright M.W. (J. Cell Biol. 2006) 2 3 64
  3. Comprehensive analysis of keratin gene clusters in humans and rodents. (PMID: 15085952) Hesse M. … Magin T.M. (Eur. J. Cell Biol. 2004) 3 4 64
  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 M.A. … Schweizer J. (Differentiation 2004) 3 4 64
  5. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PMID: 16625196) Zody M.C. … Nusbaum C. (Nature 2006) 4 64

Products for KRT39 Gene

Sources for KRT39 Gene

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