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KRT40 Gene

protein-coding   GIFtS: 43
GCID: GC17M039133

Keratin 40

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Keratin 401 2     cytokeratin-402
Type I Hair Keratin Ka362 3     Keratin, Type I Cytoskeletal 402
CK-402 3     keratin-402
K402 3     Cytokeratin-403
KA362 3     Keratin-403

External Ids:    HGNC: 267071   Entrez Gene: 1251152   Ensembl: ENSG000002048897   UniProtKB: Q6A1623   

Export aliases for KRT40 gene to outside databases

Previous GC identifers: GC17M036388 GC17M034928


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for KRT40 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 KRT40 Gene:
KRT40 (keratin 40) is a protein-coding gene. Diseases associated with KRT40 include alpha thalassemia, and thalassemia. GO annotations related to this gene include structural molecule activity. An important paralog of this gene is KRT34.

UniProtKB/Swiss-Prot: K1C40_HUMAN, Q6A162
Function: May play a role in late hair differentiation




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000017.11  NT_010783.16  NC_018928.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the KRT40 gene promoter:
         GCNF   IRF-1   LCR-F1   FOXL1   HEN1   FAC1   FOXJ2 (long isoform)   GCNF-1   FOXJ2   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKRT40 promoter sequence
   Search Chromatin IP Primers for KRT40

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KRT40


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17q21.2   Ensembl cytogenetic band:  17q21.2   HGNC cytogenetic band: 17q21.2

KRT40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KRT40 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M039133:  view genomic region     (about GC identifiers)

Start:
39,133,968 bp from pter      End:
39,143,387 bp from pter
Size:
9,420 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: K1C40_HUMAN, Q6A162 (See protein sequence)
Recommended Name: Keratin, type I cytoskeletal 40  
Size: 431 amino acids; 48139 Da
Subunit: Heterotetramer of two type I and two type II keratins
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)
Secondary accessions: Q6IFU5

Explore the universe of human proteins at neXtProt for KRT40: NX_Q6A162

Explore proteomics data for KRT40 at MOPED


See KRT40 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_872303.2  
ENSEMBL proteins: 
 ENSP00000434458   ENSP00000381500   ENSP00000366984  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
IFF1: Intermediate filaments type I, keratins (acidic)

2 InterPro protein domains:
 IPR001664 IF
 IPR002957 Keratin_I

Graphical View of Domain Structure for InterPro Entry Q6A162

ProtoNet protein and cluster: Q6A162

2 Blocks protein domains:
IPB001664 Intermediate filament protein
IPB002957 Type I keratin signature


UniProtKB/Swiss-Prot: K1C40_HUMAN, Q6A162
Similarity: Belongs to the intermediate filament family


KRT40 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: K1C40_HUMAN, Q6A162
Function: May play a role in late hair differentiation

     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005198structural molecule activity IEA--
     
KRT40 for ontologies           About GeneDecksing


Phenotypes:
     3 GenomeRNAi human phenotypes for KRT40:
 Increased G1 DNA content  Increased gamma-H2AX phosphory  Increased number of cells in m 

Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytoskeleton3
cytosol3
nucleus2

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005882intermediate filament IEA--

KRT40 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for KRT40
Interactions:

    Search GeneGlobe Interaction Network for KRT40

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for KRT40 (K1C40)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for KRT40 gene: 
NM_182497.3  

Unigene Cluster for KRT40:

Keratin 40
Hs.534929  [show with all ESTs]
Unigene Representative Sequence: NM_182497
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000461923(uc002hvq.1 uc010cxh.1) ENST00000398486 ENST00000377755

miRNA
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Additional mRNA sequence: 

AJ786658.1 BC130396.1 BC144250.1 BC150174.1 BC150191.1 

2 DOTS entries:

DT.75114219  DT.120973374 

10 AceView cDNA sequences:

AI141538 BX112843 BK004055 AX748364 AK093919 CD107509 NM_182497 CD107829 
AJ786658 CD251357 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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KRT40 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AGAAATGTCA
KRT40 Expression
About this image

KRT40 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

KRT40 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.534929

UniProtKB/Swiss-Prot: K1C40_HUMAN, Q6A162
Tissue specificity: Expressed in skin and scalp. Also very weakly expressed in tongue, breast, colon and small
intestine. In the hair follicle, it is specifically present in the upper hair cuticle. Not present in the upper
cortex (at protein level)

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In Situ
Assay Products:
 

 
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for KRT40 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Krt401 , 5 keratin 401, 5 81.71(n)1
79.53(a)1
  11 (62.92 cM)5
4062211  NM_001039666.11  NP_001034755.11 
 995374855 
lizard
(Anolis carolinensis)
Reptilia --
--
Keratin aHA1; Uncharacterized protein
42(a)
38(a)
many ↔ many
many ↔ many
6(70606275-70614367)
6(70591466-70598937)
zebrafish
(Danio rerio)
Actinopterygii wu:fb17f056
cyt16
(see all 14)
type I cytokeratin, enveloping layer
(see all 14)
41(a)
39(a)
(see all 14)
many ↔ many
many ↔ many
(see all 14)
22(11885419-11889710) ENSDARG00000095147
19(5986623-5988852) ENSDARG00000092947


ENSEMBL Gene Tree for KRT40 (if available)
TreeFam Gene Tree for KRT40 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for KRT40 gene
KRT342  KRT172  KRT162  KRT312  KRT252  KRT392  KRT202  KRT372  
KRT272  KRT322  KRT382  KRT362  KRT192  KRT282  KRT142  KRT132  
KRT262  KRT102  KRT122  KRT352  KRT152  KRT242  KRT33B2  KRT92  
KRT33A2  
Selected SIMAP similar genes for KRT40 using alignment to 3 protein entries:     K1C40_HUMAN (see all proteins) (see all similar genes):
KRT14    KRT33B    KRT33A    KRT15    KRT35    KRT13
KRT31    K14    KRT10    KRT20    KRT34    KRT36
GUCA1B    KRT18    KRTHA7    KRT32    KRT12    keratin

KRT40 for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for KRT40
PGOHUM00000237074


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for KRT40 (see all 420)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 17 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs676207131,2
C--34939744(+) ACACA-/TGCACA
CACACACG
CAAAT
1 -- us2k10--------
rs127093711,2
C,A--39133689(+) AAAAAA/TAAAAA 1 -- ds50011Minor allele frequency- T:0.00NA 2
rs98897331,2
C,A--39133696(+) AAAAAA/TAAAAA 1 -- ds50012Minor allele frequency- T:0.00NA WA 4
rs58203801,2
C--39138118(+) TAGttTTTG/-  
        
tttgt
2 -- int11Minor allele frequency- -:0.50CSA 2
rs341821811,2
C--39138119(+) AGTTT-/TTTG  
        
TTGTT
2 -- int10--------
rs30676511,2
C--39138121(+) TGTTT-/GTTT  
        
TTTGA
1 -- int10--------
rs50209041,2
C--39138918(+) GTGTGA/TGAGAG 1 -- int10--------
rs49989261,2
C--39138925(+) AGAGAC/GAGAGA 1 -- int1 trp31Minor allele frequency- G:0.00WA 2
rs58203851,2
C--39141113(+) GTGTG-/GT/GTGTGTGTGT/GTTGTGTGTGTGTGTGT/GTTGTG
TGTGTGTGTGTGTGT
/T/TG/TGTGTGTGTGTGTGTGTGTG
CAAAC
2 -- int1 cds11CSA 2
rs58203871,2
C--39142984(+) AAAAA-/ACCGAC 1 -- int11Minor allele frequency- A:0.50CSA 2

HapMap Linkage Disequilibrium report for KRT40 (39133968 - 39143387 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for KRT40:    About this table    
Variant IDTypeSubtypePubMed ID
esv22517CNV Loss19812545
nsv908230CNV Loss21882294
nsv9550CNV Loss18304495

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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2 diseases for KRT40:    
About MalaCards
alpha thalassemia    thalassemia


KRT40 for disorders           About GeneDecksing

Genetic Association Database (GAD): KRT40

Export disorders for KRT40 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for KRT40 gene integrated from 10 sources:
(articles sorted by number of sources associating them with KRT40)
    Utopia: connect your pdf to the dynamic
world of online information

  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. (PubMed id 17301834)1, 2 Langbein L.... Schweizer J. (J. Invest. Dermatol. 2007)
  2. New consensus nomenclature for mammalian keratins. (PubMed id 16831889)1, 3 Schweizer J....Wright M.W. (J. Cell Biol. 2006)
  3. Comprehensive analysis of keratin gene clusters in humans and rodents. (PubMed id 15085952)1, 2 Hesse M.... Magin T.M. (Eur. J. Cell Biol. 2004)
  4. The human type I keratin gene family: characterization of new hair follicle specific members and evaluation of the chromosome 17q21.2 gene domain. (PubMed id 15617563)1, 2 Rogers M.A.... Schweizer J. (Differentiation 2004)
  5. Genome-wide association with select biomarker traits in the Framingham Heart Study. (PubMed id 17903293)4 Benjamin E.J....Vasan R.S. (BMC Med. Genet. 2007)
  6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 125115 HGNC: 26707 AceView: KA36 Ensembl:ENSG00000204889 euGenes: HUgn125115
ECgene: KRT40 H-InvDB: KRT40

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for KRT40 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for KRT40 gene:
Search GeneIP for patents involving KRT40

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 Block miRNA regulation of human, mouse, rat KRT40 using miScript Target Protectors SeqTarget long-range PCR primers for resequencing KRT40
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 Search Tocris compounds for KRT40 (K1C40)
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

 Novus Tissue Slides
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 See all of Abcam's Antibodies, Kits and Proteins for KRT40
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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat KRT40
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for KRT40
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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