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... See more...

Aliases for KRT39 Gene

Aliases for KRT39 Gene

  • Keratin 39 2 3 5
  • KA35 2 3 4
  • Keratin, Type I Cytoskeletal 39 3 4
  • Type I Hair Keratin Ka35 3 4
  • Keratin 39, Type I 2 3
  • Cytokeratin-39 3 4
  • CK-39 3 4
  • K39 3 4
  • Keratin-39 4
  • KRT39 5

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. Diseases associated with KRT39 include Skin Pilomatrix Carcinoma and Loose Anagen Hair Syndrome. Among its related pathways are Relaxin signaling pathway 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 Summary for KRT39 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for KRT39 Gene

Genomics for KRT39 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for KRT39 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
GH17J040966 Promoter 0.3 EPDnew 250.7 0.0 -20 0.1 KRT39 HSALNG0116410 KRT40 LOC107985072 ENSG00000234477
GH17J040948 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.4 +12.2 12247 11.8 SSRP1 ATF2 KLF9 CEBPA JUND ZNF217 MXD4 CEBPB FOXA1 ZFP64 KRTAP3-2 KRT23 KRTAP2-1 KRT39 KRT40 KRTAP2-2 ENSG00000234477 KRTAP3-3 KRTAP1-5 KRTAP3-1
GH17J040935 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 6 +29.8 29847 4.6 CEBPA FOXA2 SAP130 GABPB1 FOXP1 TBP SOX5 ZNF48 ATF2 CEBPG KRT23 lnc-KRT23-1 KRT10-AS1 KRT39 KRTAP3-2 KRTAP2-1 LOC107985072 ENSG00000234477 KRT20
GH17J040980 Enhancer 0.6 Ensembl ENCODE 12.8 -13.5 -13453 2.8 MAFF MAFK POLR2A KRT39 KRT40 ENSG00000234477 KRTAP3-1 KRT23 HSALNG0116410 LOC107985072
GH17J040979 Enhancer 0.2 Ensembl 12.8 -11.5 -11453 0.8 KRT23 KRT39 KRTAP3-2 KRTAP3-1 KRT40 HSALNG0116410 LOC107985072
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KRT39 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for KRT39

Top Transcription factor binding sites by QIAGEN in the KRT39 gene promoter:
  • AML1a
  • FAC1
  • FOXF2
  • FOXO3
  • FOXO3a
  • FOXO3b
  • GCNF
  • GCNF-1
  • GCNF-2
  • Pax-5

Genomic Locations for KRT39 Gene

Latest Assembly
chr17:40,958,417-40,966,948
(GRCh38/hg38)
Size:
8,532 bases
Orientation:
Minus strand

Previous Assembly
chr17:39,114,669-39,123,200
(GRCh37/hg19 by Entrez Gene)
Size:
8,532 bases
Orientation:
Minus strand

chr17:39,114,669-39,123,144
(GRCh37/hg19 by Ensembl)
Size:
8,476 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr17(ALT_REF_LOCI_1):107,812-116,343 (-)

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:
    Q6A163-K1C39_HUMAN
    Recommended name:
    Keratin, type I cytoskeletal 39
    Protein Accession:
    Q6A163
    Secondary Accessions:
    • B2RXK6
    • Q6IFU6

    Protein attributes for KRT39 Gene

    Size:
    491 amino acids
    Molecular mass:
    55651 Da
    Quaternary structure:
    • Heterotetramer of two type I and two type II keratins.
    Miscellaneous:
    • 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

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

Protein Domains for KRT39 Gene

InterPro:
Blocks:
  • Intermediate filament protein
  • Type I keratin signature

Suggested Antigen Peptide Sequences for KRT39 Gene

GenScript: Design optimal peptide antigens:
  • Type I hair keratin Ka35 (K1C39_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6A163

UniProtKB/Swiss-Prot:

K1C39_HUMAN :
  • Belongs to the intermediate filament family.
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.

Phenotypes From GWAS Catalog for KRT39 Gene

Gene Ontology (GO) - Molecular Function for KRT39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IEA --
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with KRT39: view
genes like me logo Genes that share phenotypes with KRT39: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KRT39

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

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 KRT39 gene
Compartment Confidence
cytosol 5
cytoskeleton 3
nucleus 1
golgi apparatus 1
extracellular 0
peroxisome 0

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

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

Pathways by source for KRT39 Gene

2 Reactome pathways 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 :
4 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KRT39

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

No ASD Table

Relevant External Links for KRT39 Gene

GeneLoc Exon Structure for
KRT39

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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for KRT39

SOURCE GeneReport for Unigene cluster for KRT39 Gene:

Hs.28467

mRNA Expression by UniProt/SwissProt for KRT39 Gene:

Q6A163-K1C39_HUMAN
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 for research

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
Chimpanzee
(Pan troglodytes)
Mammalia KRT39 29 30
  • 99.19 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia KRT39 29 30
  • 83.51 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia KRT39 29 30
  • 83.23 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Krt39 29
  • 79.9 (n)
Mouse
(Mus musculus)
Mammalia Krt39 29 16 30
  • 79.86 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia KRT39 30
  • 57 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia KRT39 30
  • 56 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 49 (a)
ManyToMany
-- 30
  • 40 (a)
ManyToMany
Zebrafish
(Danio rerio)
Actinopterygii cyt1l 30
  • 38 (a)
ManyToMany
zgc:109868 30
  • 38 (a)
ManyToMany
cyt1 30
  • 38 (a)
ManyToMany
krt17 30
  • 37 (a)
ManyToMany
zgc:92061 30
  • 37 (a)
ManyToMany
wu:fb17f05 30
  • 37 (a)
ManyToMany
zgc:153629 30
  • 35 (a)
ManyToMany
krt1-19d 30
  • 35 (a)
ManyToMany
zgc:136902 30
  • 34 (a)
ManyToMany
zgc:92035 30
  • 34 (a)
ManyToMany
krt15 30
  • 33 (a)
ManyToMany
si:dkeyp-113d7.4 30
  • 32 (a)
ManyToMany
BX469912.1 30
  • 19 (a)
ManyToMany
zgc:92533 30
  • 19 (a)
ManyToMany
Species where no ortholog for KRT39 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for KRT39 (if available)
TreeFam:
Gene Tree for KRT39 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for KRT39: view image
Alliance of Genome Resources:
Additional Orthologs for KRT39

Paralogs for KRT39 Gene

(35) SIMAP similar genes for KRT39 Gene using alignment to 2 proteins:

  • K1C39_HUMAN
  • J3QRE9_HUMAN
genes like me logo Genes that share paralogs with KRT39: view

Variants for KRT39 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for KRT39 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs483352776 Uncertain Significance: not provided 40,958,616(-) T/G
NM_213656.4(KRT39):c.1461A>C (p.Arg487Ser)
MISSENSE
rs17843021 -- p.Thr341Met
rs17843023 -- p.Leu383Met
rs7213256 -- p.Arg456Gln

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for KRT39 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for KRT39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
KRT39
Leiden Open Variation Database (LOVD)
KRT39

SNP Genotyping and Copy Number Assays for research

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

Disorders for KRT39 Gene

MalaCards: The human disease database

(3) MalaCards diseases for KRT39 Gene - From: COP

Disorder Aliases PubMed IDs
skin pilomatrix carcinoma
  • malignant pilomatricoma
loose anagen hair syndrome
  • loose anagen syndrome
white sponge nevus 1
  • wsn1
- elite association - COSMIC cancer census association via MalaCards
Search KRT39 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for KRT39

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

No data available for 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
  2. New consensus nomenclature for mammalian keratins. (PMID: 16831889) Schweizer J … Wright MW (The Journal of cell biology 2006) 2 3
  3. 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
  4. Comprehensive analysis of keratin gene clusters in humans and rodents. (PMID: 15085952) Hesse M … Magin TM (European journal of cell biology 2004) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for KRT39 Gene

Sources for KRT39 Gene