Human Gene CASP6 (uc003hzn.1)
  Description: Homo sapiens caspase 6, apoptosis-related cysteine peptidase (CASP6), transcript variant alpha, mRNA.
RefSeq Summary (NM_001226): This gene encodes a member of the cysteine-aspartic acid protease (caspase) family of enzymes. Sequential activation of caspases plays a central role in the execution-phase of cell apoptosis. Caspases exist as inactive proenzymes which undergo proteolytic processing at conserved aspartic acid residues to produce two subunits, large and small, that dimerize to form the active enzyme. This protein is processed by caspases 7, 8 and 10, and is thought to function as a downstream enzyme in the caspase activation cascade. Alternative splicing of this gene results in multiple transcript variants that encode different isoforms. [provided by RefSeq, Oct 2015].
Transcript (Including UTRs)
   Position: hg19 chr4:110,609,785-110,624,629 Size: 14,845 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr4:110,610,486-110,624,551 Size: 14,066 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:110,609,785-110,624,629)mRNA (may differ from genome)Protein (293 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CASP6_HUMAN
DESCRIPTION: RecName: Full=Caspase-6; Short=CASP-6; EC=3.4.22.59; AltName: Full=Apoptotic protease Mch-2; Contains: RecName: Full=Caspase-6 subunit p18; Contains: RecName: Full=Caspase-6 subunit p11; Flags: Precursor;
FUNCTION: Involved in the activation cascade of caspases responsible for apoptosis execution. Cleaves poly(ADP-ribose) polymerase in vitro, as well as lamins. Overexpression promotes programmed cell death.
CATALYTIC ACTIVITY: Strict requirement for Asp at position P1 and has a preferred cleavage sequence of Val-Glu-His-Asp-|-.
ENZYME REGULATION: Activation is suppressed by phosphorylation at Ser-257.
SUBUNIT: Heterotetramer that consists of two anti-parallel arranged heterodimers, each one formed by a 18 kDa (p18) and a 11 kDa (p11) subunit. Interacts with BIRC6/bruce.
INTERACTION: Q01826:SATB1; NbExp=2; IntAct=EBI-718729, EBI-743747;
SUBCELLULAR LOCATION: Cytoplasm.
PTM: Cleavages by caspase-3, caspase-8 or -10 generate the two active subunits.
SIMILARITY: Belongs to the peptidase C14A family.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/casp6/";

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CASP6
CDC HuGE Published Literature: CASP6
Positive Disease Associations: Body Height , Breath Tests
Related Studies:
  1. Body Height
    , , . [PubMed 0]
  2. Breath Tests
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: CASP6
Diseases sorted by gene-association score: dystrophinopathies (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 16.29 RPKM in Colon - Transverse
Total median expression: 198.37 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -40.0078-0.513 Picture PostScript Text
3' UTR -195.80701-0.279 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
IPR015469 - Caspase_6
IPR011600 - Pept_C14_cat
IPR001309 - Pept_C14_ICE_p20
IPR016129 - Pept_C14_ICE_p20_AS
IPR002138 - Pept_C14_p10
IPR002398 - Pept_C14_p45
IPR015917 - Pept_C14_p45_core

Pfam Domains:
PF00656 - Caspase domain

SCOP Domains:
52129 - Caspase-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1MI9 - Model 2WDP - X-ray MuPIT 3K7E - X-ray MuPIT 3NKF - X-ray 3NR2 - X-ray MuPIT 3OD5 - X-ray MuPIT 3P45 - X-ray MuPIT 3P4U - X-ray MuPIT 3QNW - X-ray MuPIT 3S70 - X-ray MuPIT 3S8E - X-ray MuPIT 3V6L - X-ray MuPIT 3V6M - X-ray MuPIT 4EJF - X-ray MuPIT 4FXO - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P55212
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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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004175 endopeptidase activity
GO:0004197 cysteine-type endopeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
GO:0097200 cysteine-type endopeptidase activity involved in execution phase of apoptosis

Biological Process:
GO:0006508 proteolysis
GO:0006915 apoptotic process
GO:0030855 epithelial cell differentiation
GO:0042981 regulation of apoptotic process
GO:0072734 cellular response to staurosporine
GO:0097194 execution phase of apoptosis

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  U20537 - Human cysteine protease Mch2 isoform beta (Mch2) mRNA, complete cds.
U20536 - Human cysteine protease Mch2 isoform alpha (Mch2) mRNA, complete cds.
BC000305 - Homo sapiens caspase 6, apoptosis-related cysteine peptidase, mRNA (cDNA clone MGC:8388 IMAGE:2820468), complete cds.
BC004460 - Homo sapiens caspase 6, apoptosis-related cysteine peptidase, mRNA (cDNA clone MGC:4318 IMAGE:2820468), complete cds.
JD348789 - Sequence 329813 from Patent EP1572962.
JD219873 - Sequence 200897 from Patent EP1572962.
JD042322 - Sequence 23346 from Patent EP1572962.
JD117206 - Sequence 98230 from Patent EP1572962.
JD534803 - Sequence 515827 from Patent EP1572962.
JD292566 - Sequence 273590 from Patent EP1572962.
JD092091 - Sequence 73115 from Patent EP1572962.
JD341915 - Sequence 322939 from Patent EP1572962.
JD445178 - Sequence 426202 from Patent EP1572962.
JD321137 - Sequence 302161 from Patent EP1572962.
JD041396 - Sequence 22420 from Patent EP1572962.
JD169377 - Sequence 150401 from Patent EP1572962.
JD529242 - Sequence 510266 from Patent EP1572962.
JD557391 - Sequence 538415 from Patent EP1572962.
JD430210 - Sequence 411234 from Patent EP1572962.
JD118455 - Sequence 99479 from Patent EP1572962.
JD326827 - Sequence 307851 from Patent EP1572962.
JD378189 - Sequence 359213 from Patent EP1572962.
JD455042 - Sequence 436066 from Patent EP1572962.
JD478071 - Sequence 459095 from Patent EP1572962.
JD407220 - Sequence 388244 from Patent EP1572962.
JD111762 - Sequence 92786 from Patent EP1572962.
JD264151 - Sequence 245175 from Patent EP1572962.
JD420136 - Sequence 401160 from Patent EP1572962.
JD105305 - Sequence 86329 from Patent EP1572962.
JD180527 - Sequence 161551 from Patent EP1572962.
JD144779 - Sequence 125803 from Patent EP1572962.
JD434174 - Sequence 415198 from Patent EP1572962.
JD269212 - Sequence 250236 from Patent EP1572962.
EU176306 - Synthetic construct Homo sapiens clone IMAGE:100006385; FLH176730.01X; RZPDo839E04251D caspase 6, apoptosis-related cysteine peptidase (CASP6) gene, encodes complete protein.
KJ890828 - Synthetic construct Homo sapiens clone ccsbBroadEn_00222 CASP6 gene, encodes complete protein.
DQ894589 - Synthetic construct Homo sapiens clone IMAGE:100009049; FLH176724.01L; RZPDo839G08121D caspase 6, apoptosis-related cysteine peptidase (CASP6) gene, encodes complete protein.
AB590350 - Synthetic construct DNA, clone: pFN21AE1445, Homo sapiens CASP6 gene for caspase 6, apoptosis-related cysteine peptidase, without stop codon, in Flexi system.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04210 - Apoptosis

BioCarta from NCI Cancer Genome Anatomy Project
h_deathPathway - Induction of apoptosis through DR3 and DR4/5 Death Receptors
h_mitochondriaPathway - Role of Mitochondria in Apoptotic Signaling
h_caspasePathway - Caspase Cascade in Apoptosis
h_HivnefPathway - HIV-I Nef: negative effector of Fas and TNF
h_chemicalPathway - Apoptotic Signaling in Response to DNA Damage
h_fasPathway - FAS signaling pathway ( CD95 )

Reactome (by CSHL, EBI, and GO)

Protein P55212 (Reactome details) participates in the following event(s):

R-HSA-350318 Caspase-mediated cleavage of vimentin at TNLD (429)
R-HSA-264865 Caspase-mediated cleavage of Lamin A
R-HSA-264871 Caspase-mediated cleavage of Lamin B1
R-HSA-352268 Cleavage of Satb1
R-HSA-6803207 TP53 Regulates Transcription of Caspase Activators and Caspases
R-HSA-5633008 TP53 Regulates Transcription of Cell Death Genes
R-HSA-352238 Breakdown of the nuclear lamina
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-111465 Apoptotic cleavage of cellular proteins
R-HSA-264870 Caspase-mediated cleavage of cytoskeletal proteins
R-HSA-212436 Generic Transcription Pathway
R-HSA-75153 Apoptotic execution phase
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-109581 Apoptosis
R-HSA-74160 Gene expression (Transcription)
R-HSA-5357801 Programmed Cell Death

-  Other Names for This Gene
  Alternate Gene Symbols: CASP6_HUMAN, MCH2, NM_001226, NP_001217, P55212, Q9BQE7
UCSC ID: uc003hzn.1
RefSeq Accession: NM_001226
Protein: P55212 (aka CASP6_HUMAN or ICE6_HUMAN)
CCDS: CCDS3684.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001226.3
exon count: 7CDS single in 3' UTR: no RNA size: 1661
ORF size: 882CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1804.00frame shift in genome: no % Coverage: 100.00
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.