Human Gene KRT39 (ENST00000355612.7_7) from GENCODE V47lift37
  Description: keratin 39 (from RefSeq NM_213656.4)
Gencode Transcript: ENST00000355612.7_7
Gencode Gene: ENSG00000196859.8_9
Transcript (Including UTRs)
   Position: hg19 chr17:39,114,669-39,123,200 Size: 8,532 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr17:39,114,853-39,123,108 Size: 8,256 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:39,114,669-39,123,200)mRNA (may differ from genome)Protein (491 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: K1C39_HUMAN
DESCRIPTION: RecName: Full=Keratin, type I cytoskeletal 39; AltName: Full=Cytokeratin-39; Short=CK-39; AltName: Full=Keratin-39; Short=K39; AltName: Full=Type I hair keratin Ka35;
FUNCTION: May play a role in late hair differentiation.
SUBUNIT: Heterotetramer of two type I and two type II keratins.
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).
DEVELOPMENTAL STAGE: During differentiation of the hair, it is one of the last keratins expressed.
MISCELLANEOUS: There are two types of cytoskeletal and microfibrillar keratin, I (acidic) and II (neutral to basic) (40- 55 and 56-70 kDa, respectively).
SIMILARITY: Belongs to the intermediate filament family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.25 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 0.83 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -22.3092-0.242 Picture PostScript Text
3' UTR -33.90184-0.184 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016044 - F
IPR001664 - IF
IPR018039 - Intermediate_filament_CS
IPR002957 - Keratin_I

Pfam Domains:
PF00038 - Intermediate filament protein

SCOP Domains:
46579 - Prefoldin
64593 - Intermediate filament protein, coiled coil region

ModBase Predicted Comparative 3D Structure on Q6A163
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005198 structural molecule activity

Biological Process:
GO:0031424 keratinization
GO:0070268 cornification

Cellular Component:
GO:0005829 cytosol
GO:0005882 intermediate filament


-  Descriptions from all associated GenBank mRNAs
  BC160073 - Synthetic construct Homo sapiens clone IMAGE:100064009, MGC:193188 keratin 39 (KRT39) mRNA, encodes complete protein.
AJ786657 - Homo sapiens mRNA for Ka35 protein.
BC157887 - Homo sapiens keratin 39, mRNA (cDNA clone MGC:189711 IMAGE:8862708), complete cds.
BC171907 - Homo sapiens cDNA clone IMAGE:9054561.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6A163 (Reactome details) participates in the following event(s):

R-HSA-6805546 Keratin type I binds keratin type II
R-HSA-6805573 Keratin type I/type II heterodimers form tetramers
R-HSA-6806613 Keratin tetramers bind to form unit length filaments
R-HSA-6805567 Keratinization
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: B2RXK6, ENST00000355612.1, ENST00000355612.2, ENST00000355612.3, ENST00000355612.4, ENST00000355612.5, ENST00000355612.6, K1C39_HUMAN, KA35, NM_213656, Q6A163, Q6IFU6, uc317zdw.1, uc317zdw.2
UCSC ID: ENST00000355612.7_7
RefSeq Accession: NM_213656.4
Protein: Q6A163 (aka K1C39_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.