Human Gene CTSS (ENST00000368985.8_7) from GENCODE V47lift37
  Description: cathepsin S, transcript variant 1 (from RefSeq NM_004079.5)
Gencode Transcript: ENST00000368985.8_7
Gencode Gene: ENSG00000163131.12_14
Transcript (Including UTRs)
   Position: hg19 chr1:150,702,664-150,738,254 Size: 35,591 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr1:150,705,522-150,737,239 Size: 31,718 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:150,702,664-150,738,254)mRNA (may differ from genome)Protein (331 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CATS_HUMAN
DESCRIPTION: RecName: Full=Cathepsin S; EC=3.4.22.27; Flags: Precursor;
FUNCTION: Thiol protease. Key protease responsible for the removal of the invariant chain from MHC class II molecules. The bond- specificity of this proteinase is in part similar to the specificities of cathepsin L and cathepsin N.
CATALYTIC ACTIVITY: Similar to cathepsin L, but with much less activity on Z-Phe-Arg-|-NHMec, and more activity on the Z-Val-Val- Arg-|-Xaa compound.
SUBUNIT: Monomer.
SUBCELLULAR LOCATION: Lysosome.
SIMILARITY: Belongs to the peptidase C1 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


-  MalaCards Disease Associations
  MalaCards Gene Search: CTSS
Diseases sorted by gene-association score: cercarial dermatitis (2), mandibular cancer (2), non-suppurative otitis media (1), jaw cancer (1), periodontosis (1), corneal dystrophy, subepithelial mucinous (1), cerebellopontine angle tumor (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • D004317 Doxorubicin
  • D004958 Estradiol
  • D004997 Ethinyl Estradiol
  • D008727 Methotrexate
  • D013749 Tetrachlorodibenzodioxin
  • D014640 Vancomycin
  • C049325 1,2-dithiol-3-thione
  • D015058 1-Naphthylisothiocyanate
  • C518576 2-methylbutyric acid 4-((1,3)dioxan-5-ylmethoxyimino)-8-(2-(4-hydroxy-6-oxo-tetrahydropyran-2-yl)ethyl -7-methyl-6-oxo-1,2,3,4,6,7,8,8a-octahydronaphthyl)heptanoate
          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: 149.95 RPKM in Whole Blood
Total median expression: 568.93 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 -16.0082-0.195 Picture PostScript Text
3' UTR -929.302858-0.325 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
IPR025661 - Pept_asp_AS
IPR000169 - Pept_cys_AS
IPR025660 - Pept_his_AS
IPR013128 - Peptidase_C1A
IPR000668 - Peptidase_C1A_C
IPR013201 - Prot_inhib_I29

Pfam Domains:
PF00112 - Papain family cysteine protease
PF08246 - Cathepsin propeptide inhibitor domain (I29)

SCOP Domains:
54001 - Cysteine proteinases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1BXF - Model 1GLO - X-ray MuPIT 1MS6 - X-ray MuPIT 1NPZ - X-ray 1NQC - X-ray 2C0Y - X-ray MuPIT 2F1G - X-ray MuPIT 2FQ9 - X-ray MuPIT 2FRA - X-ray MuPIT 2FRQ - X-ray MuPIT 2FT2 - X-ray MuPIT 2FUD - X-ray MuPIT 2FYE - X-ray MuPIT 2G6D - X-ray MuPIT 2G7Y - X-ray MuPIT 2H7J - X-ray MuPIT 2HH5 - X-ray MuPIT 2HHN - X-ray MuPIT 2HXZ - X-ray MuPIT 2OP3 - X-ray MuPIT 2R9M - X-ray MuPIT 2R9N - X-ray MuPIT 2R9O - X-ray MuPIT 3IEJ - X-ray MuPIT 3KWN - X-ray 3MPE - X-ray 3MPF - X-ray 3N3G - X-ray MuPIT 3N4C - X-ray MuPIT 3OVX - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P25774
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001968 fibronectin binding
GO:0004197 cysteine-type endopeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005518 collagen binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity
GO:0043236 laminin binding
GO:0043394 proteoglycan binding

Biological Process:
GO:0002224 toll-like receptor signaling pathway
GO:0002250 adaptive immune response
GO:0006508 proteolysis
GO:0006955 immune response
GO:0010447 response to acidic pH
GO:0016485 protein processing
GO:0019882 antigen processing and presentation
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0022617 extracellular matrix disassembly
GO:0030574 collagen catabolic process
GO:0034769 basement membrane disassembly
GO:0043312 neutrophil degranulation
GO:0048002 antigen processing and presentation of peptide antigen
GO:0051603 proteolysis involved in cellular protein catabolic process
GO:0097067 cellular response to thyroid hormone stimulus
GO:2001259 positive regulation of cation channel activity

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005764 lysosome
GO:0036021 endolysosome lumen
GO:0043202 lysosomal lumen
GO:0043231 intracellular membrane-bounded organelle
GO:1904724 tertiary granule lumen
GO:1904813 ficolin-1-rich granule lumen


-  Descriptions from all associated GenBank mRNAs
  LF383811 - JP 2014500723-A/191314: Polycomb-Associated Non-Coding RNAs.
AK226095 - Homo sapiens mRNA for cathepsin S preproprotein variant, clone: ej00690.
BC002642 - Homo sapiens cathepsin S, mRNA (cDNA clone MGC:3886 IMAGE:3610589), complete cds.
M90696 - Homo sapiens cathepsin S (CTSS) mRNA, complete cds.
AK301472 - Homo sapiens cDNA FLJ50259 complete cds, highly similar to Cathepsin S precursor (EC 3.4.22.27).
M86553 - Human cathepsin S mRNA, complete cds.
S93414 - cathepsin S=elastinolytic cysteine protease [human, alveolar macrophages, mRNA, 1255 nt].
CR541676 - Homo sapiens full open reading frame cDNA clone RZPDo834D0328D for gene CTSS, cathepsin S; complete cds, incl. stopcodon.
AK314482 - Homo sapiens cDNA, FLJ95290, highly similar to Homo sapiens cathepsin S (CTSS), mRNA.
AB527651 - Synthetic construct DNA, clone: pF1KB5654, Homo sapiens CTSS gene for cathepsin S, without stop codon, in Flexi system.
KJ901031 - Synthetic construct Homo sapiens clone ccsbBroadEn_10425 CTSS gene, encodes complete protein.
MA619388 - JP 2018138019-A/191314: Polycomb-Associated Non-Coding RNAs.
AK024855 - Homo sapiens cDNA: FLJ21202 fis, clone COL00293.
JD411345 - Sequence 392369 from Patent EP1572962.
JD561920 - Sequence 542944 from Patent EP1572962.
JD400791 - Sequence 381815 from Patent EP1572962.
JD236804 - Sequence 217828 from Patent EP1572962.
JD133754 - Sequence 114778 from Patent EP1572962.
JD208091 - Sequence 189115 from Patent EP1572962.
JD315206 - Sequence 296230 from Patent EP1572962.
JD305938 - Sequence 286962 from Patent EP1572962.
JD365873 - Sequence 346897 from Patent EP1572962.
JD505903 - Sequence 486927 from Patent EP1572962.
JD356424 - Sequence 337448 from Patent EP1572962.
JD311611 - Sequence 292635 from Patent EP1572962.
JD311612 - Sequence 292636 from Patent EP1572962.
JD311610 - Sequence 292634 from Patent EP1572962.
JD414738 - Sequence 395762 from Patent EP1572962.
JD311609 - Sequence 292633 from Patent EP1572962.
JD476698 - Sequence 457722 from Patent EP1572962.
JD069716 - Sequence 50740 from Patent EP1572962.
JD256521 - Sequence 237545 from Patent EP1572962.
JD383762 - Sequence 364786 from Patent EP1572962.
JD147927 - Sequence 128951 from Patent EP1572962.
JD524920 - Sequence 505944 from Patent EP1572962.
JD352644 - Sequence 333668 from Patent EP1572962.
JD350631 - Sequence 331655 from Patent EP1572962.
JD110059 - Sequence 91083 from Patent EP1572962.
JD149790 - Sequence 130814 from Patent EP1572962.
JD114355 - Sequence 95379 from Patent EP1572962.
JD048890 - Sequence 29914 from Patent EP1572962.
JD388422 - Sequence 369446 from Patent EP1572962.
JD457182 - Sequence 438206 from Patent EP1572962.
JD335381 - Sequence 316405 from Patent EP1572962.
JD442971 - Sequence 423995 from Patent EP1572962.
JD065014 - Sequence 46038 from Patent EP1572962.
JD043663 - Sequence 24687 from Patent EP1572962.
JD049545 - Sequence 30569 from Patent EP1572962.
JD512388 - Sequence 493412 from Patent EP1572962.
JD350898 - Sequence 331922 from Patent EP1572962.
JD206709 - Sequence 187733 from Patent EP1572962.
JD178622 - Sequence 159646 from Patent EP1572962.
JD236761 - Sequence 217785 from Patent EP1572962.
JD373400 - Sequence 354424 from Patent EP1572962.
JD319379 - Sequence 300403 from Patent EP1572962.
JD043112 - Sequence 24136 from Patent EP1572962.
JD341202 - Sequence 322226 from Patent EP1572962.
JD241628 - Sequence 222652 from Patent EP1572962.
JD530552 - Sequence 511576 from Patent EP1572962.
JD472275 - Sequence 453299 from Patent EP1572962.
JD294068 - Sequence 275092 from Patent EP1572962.
JD432461 - Sequence 413485 from Patent EP1572962.
JD102037 - Sequence 83061 from Patent EP1572962.
JD352613 - Sequence 333637 from Patent EP1572962.
JD240810 - Sequence 221834 from Patent EP1572962.
JD280436 - Sequence 261460 from Patent EP1572962.
JD160368 - Sequence 141392 from Patent EP1572962.
JD502642 - Sequence 483666 from Patent EP1572962.
JD284139 - Sequence 265163 from Patent EP1572962.
JD179473 - Sequence 160497 from Patent EP1572962.
JD431192 - Sequence 412216 from Patent EP1572962.
JD074925 - Sequence 55949 from Patent EP1572962.
JD452987 - Sequence 434011 from Patent EP1572962.
JD380935 - Sequence 361959 from Patent EP1572962.
JD022571 - Sequence 3595 from Patent EP1572962.
JD240569 - Sequence 221593 from Patent EP1572962.
JD035973 - Sequence 16997 from Patent EP1572962.
LF352532 - JP 2014500723-A/160035: Polycomb-Associated Non-Coding RNAs.
LF352531 - JP 2014500723-A/160034: Polycomb-Associated Non-Coding RNAs.
LF352530 - JP 2014500723-A/160033: Polycomb-Associated Non-Coding RNAs.
LF352529 - JP 2014500723-A/160032: Polycomb-Associated Non-Coding RNAs.
LF352528 - JP 2014500723-A/160031: Polycomb-Associated Non-Coding RNAs.
LF352527 - JP 2014500723-A/160030: Polycomb-Associated Non-Coding RNAs.
MA588109 - JP 2018138019-A/160035: Polycomb-Associated Non-Coding RNAs.
MA588108 - JP 2018138019-A/160034: Polycomb-Associated Non-Coding RNAs.
MA588107 - JP 2018138019-A/160033: Polycomb-Associated Non-Coding RNAs.
MA588106 - JP 2018138019-A/160032: Polycomb-Associated Non-Coding RNAs.
MA588105 - JP 2018138019-A/160031: Polycomb-Associated Non-Coding RNAs.
MA588104 - JP 2018138019-A/160030: Polycomb-Associated Non-Coding RNAs.
LF352526 - JP 2014500723-A/160029: Polycomb-Associated Non-Coding RNAs.
JD153776 - Sequence 134800 from Patent EP1572962.
JD273844 - Sequence 254868 from Patent EP1572962.
MA588103 - JP 2018138019-A/160029: Polycomb-Associated Non-Coding RNAs.

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

Protein P25774 (Reactome details) participates in the following event(s):

R-HSA-6800434 Exocytosis of ficolin-rich granule lumen proteins
R-HSA-6798745 Exocytosis of tertiary granule lumen proteins
R-HSA-2130504 Cleavage of lip22 to lip10
R-HSA-2130349 Generation of CLIP from lip10
R-HSA-2130706 MHC class II antigen processing
R-HSA-1236948 Antigen processing by cathepsin S in endosoytic vesicle
R-HSA-1678981 TLR9 processing at neutral pH
R-HSA-1566981 Fibronectin degradation by MMP1, 3, 7, 12, 13, 19, CTSS
R-HSA-2534160 HSPG2 (perlecan) degradation by MMP13, CTSS
R-HSA-2213200 Release of endostatin-like peptides
R-HSA-1678920 TLR processing at low pH
R-HSA-6798695 Neutrophil degranulation
R-HSA-2132295 MHC class II antigen presentation
R-HSA-1236977 Endosomal/Vacuolar pathway
R-HSA-1679131 Trafficking and processing of endosomal TLR
R-HSA-1474228 Degradation of the extracellular matrix
R-HSA-2022090 Assembly of collagen fibrils and other multimeric structures
R-HSA-168249 Innate Immune System
R-HSA-1280218 Adaptive Immune System
R-HSA-1236975 Antigen processing-Cross presentation
R-HSA-168898 Toll-Like Receptors Cascades
R-HSA-1474244 Extracellular matrix organization
R-HSA-1474290 Collagen formation
R-HSA-168256 Immune System
R-HSA-983169 Class I MHC mediated antigen processing & presentation

-  Other Names for This Gene
  Alternate Gene Symbols: B4DWC9, CATS_HUMAN, D3DV05, ENST00000368985.1, ENST00000368985.2, ENST00000368985.3, ENST00000368985.4, ENST00000368985.5, ENST00000368985.6, ENST00000368985.7, NM_004079, P25774, Q5T5I0, Q6FHS5, Q9BUG3, uc318hfx.1, uc318hfx.2
UCSC ID: ENST00000368985.8_7
RefSeq Accession: NM_004079.5
Protein: P25774 (aka CATS_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.