Human Gene KRT78 (uc001sbc.1)
  Description: Homo sapiens keratin 78 (KRT78), mRNA.
RefSeq Summary (NM_173352): This gene is a member of the type II keratin gene family and encodes a protein with an intermediate filament domain. Keratins are the major structural proteins in epithelial cells, forming a cytoplasmic network of 10 to 12 nm wide intermediate filaments and creating a scaffold that gives cells the ability to withstand mechanical and non-mechanical stresses. The genes of the type II keratin family are located as a gene cluster at 12p13.13. Four pseudogenes of this gene family have been identified. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr12:53,232,746-53,242,778 Size: 10,033 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr12:53,232,897-53,242,714 Size: 9,818 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:53,232,746-53,242,778)mRNA (may differ from genome)Protein (520 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: K2C78_HUMAN
DESCRIPTION: RecName: Full=Keratin, type II cytoskeletal 78; AltName: Full=Cytokeratin-78; Short=CK-78; AltName: Full=Keratin-5b; AltName: Full=Keratin-78; Short=K78; AltName: Full=Type-II keratin Kb40;
SUBUNIT: Heterotetramer of two type I and two type II keratins.
TISSUE SPECIFICITY: Expressed in tongue, but not in skin or in any other tissues or organs examined.
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.
SEQUENCE CAUTION: Sequence=DAA00377.1; Type=Erroneous gene model prediction;

-  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: 235.53 RPKM in Esophagus - Mucosa
Total median expression: 351.67 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -10.7064-0.167 Picture PostScript Text
3' UTR -34.21151-0.227 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
IPR003054 - Keratin_II

Pfam Domains:
PF00038 - Intermediate filament protein
PF16208 - Keratin type II head

ModBase Predicted Comparative 3D Structure on Q8N1N4
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 Details     
Gene Sorter     
      
      
      

-  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:0005615 extracellular space
GO:0005829 cytosol
GO:0005882 intermediate filament
GO:0045095 keratin filament
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BX647095 - Homo sapiens mRNA; cDNA DKFZp686B15196 (from clone DKFZp686B15196).
AK096419 - Homo sapiens cDNA FLJ39100 fis, clone NTONG2001587, moderately similar to KERATIN, TYPE II CYTOSKELETAL 4.
AX721217 - Sequence 177 from Patent WO0220754.
AK298636 - Homo sapiens cDNA FLJ54374 complete cds, highly similar to Homo sapiens keratin 78 (KRT78), mRNA.
AK290901 - Homo sapiens cDNA FLJ77942 complete cds, highly similar to Homo sapiens keratin 5b (K5B), mRNA.
BC141554 - Synthetic construct Homo sapiens clone IMAGE:100014573, MGC:175315 keratin 78 (KRT78) mRNA, encodes complete protein.
AB463817 - Synthetic construct DNA, clone: pF1KB7246, Homo sapiens KRT78 gene for keratin 78, without stop codon, in Flexi system.
JD068434 - Sequence 49458 from Patent EP1572962.
JD031368 - Sequence 12392 from Patent EP1572962.
JD270124 - Sequence 251148 from Patent EP1572962.
JD200585 - Sequence 181609 from Patent EP1572962.
JD338821 - Sequence 319845 from Patent EP1572962.
JD226915 - Sequence 207939 from Patent EP1572962.
JD547348 - Sequence 528372 from Patent EP1572962.

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

Protein Q8N1N4 (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: A8K4D6, K2C78_HUMAN, K5B, KB40, NM_173352, NP_775487, Q5HYM7, Q7RTT2, Q8N1N4
UCSC ID: uc001sbc.1
RefSeq Accession: NM_173352
Protein: Q8N1N4 (aka K2C78_HUMAN)
CCDS: CCDS8840.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_173352.2
exon count: 9CDS single in 3' UTR: no RNA size: 1785
ORF size: 1563CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3182.00frame shift in genome: no % Coverage: 99.61
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.