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CSTB cystatin B [ Homo sapiens (human) ]

Gene ID: 1476, updated on 9-Dec-2018

Summary

Official Symbol
CSTBprovided by HGNC
Official Full Name
cystatin Bprovided by HGNC
Primary source
HGNC:HGNC:2482
See related
Ensembl:ENSG00000160213 MIM:601145
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PME; ULD; CST6; EPM1; STFB; CPI-B; EPM1A
Summary
The cystatin superfamily encompasses proteins that contain multiple cystatin-like sequences. Some of the members are active cysteine protease inhibitors, while others have lost or perhaps never acquired this inhibitory activity. There are three inhibitory families in the superfamily, including the type 1 cystatins (stefins), type 2 cystatins and kininogens. This gene encodes a stefin that functions as an intracellular thiol protease inhibitor. The protein is able to form a dimer stabilized by noncovalent forces, inhibiting papain and cathepsins l, h and b. The protein is thought to play a role in protecting against the proteases leaking from lysosomes. Evidence indicates that mutations in this gene are responsible for the primary defects in patients with progressive myoclonic epilepsy (EPM1). One type of mutation responsible for EPM1 is the expansion in the promoter region of this gene of a CCCCGCCCCGCG repeat from 2-3 copies to 30-78 copies. [provided by RefSeq, Jul 2016]
Expression
Biased expression in esophagus (RPKM 2096.4) and urinary bladder (RPKM 80.5) See more
Orthologs

Genomic context

See CSTB in Genome Data Viewer
Location:
21q22.3
Exon count:
3
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 21 NC_000021.9 (43773665..43776375, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45193546..45196256, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene pyridoxal kinase Neighboring gene uncharacterized LOC105372824 Neighboring gene PDXK-CSTB intergenic CAGE-defined low expression enhancer Neighboring gene cystatin B upstream repeat instability region Neighboring gene uncharacterized LOC105372825

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 infection upregulates cathepsin B, cystatin B, and cystatin C in the frontal white matter of patients with HIV-Associated Neurocognitive Disorders PubMed
HIV-1 infection upregulates cystatin B (CSTB) in microglia PubMed
HIV-1 replication requires CSTB (cystatin B) expression as shown through siRNA knockdown PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
cysteine-type endopeptidase inhibitor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cysteine-type endopeptidase inhibitor activity IDA
Inferred from Direct Assay
more info
PubMed 
endopeptidase inhibitor activity TAS
Traceable Author Statement
more info
PubMed 
protease binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
 
negative regulation of endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
negative regulation of peptidase activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of proteolysis IDA
Inferred from Direct Assay
more info
PubMed 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
collagen-containing extracellular matrix HDA PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
extracellular exosome HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space HDA PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
ficolin-1-rich granule lumen TAS
Traceable Author Statement
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
secretory granule lumen TAS
Traceable Author Statement
more info
 
tertiary granule lumen TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
cystatin-B
Names
cystatin B (stefin B)
epididymis secretory sperm binding protein
liver thiol proteinase inhibitor

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011545.1 RefSeqGene

    Range
    5004..7714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_485

mRNA and Protein(s)

  1. NM_000100.3NP_000091.1  cystatin-B

    See identical proteins and their annotated locations for NP_000091.1

    Status: REVIEWED

    Source sequence(s)
    AP001053, BC003370, BX419549, CD364415
    Consensus CDS
    CCDS13701.1
    UniProtKB/Swiss-Prot
    P04080
    UniProtKB/TrEMBL
    Q76LA1
    Related
    ENSP00000291568.5, ENST00000291568.6
    Conserved Domains (1) summary
    pfam00031
    Location:492
    Cystatin; Cystatin domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p12 Primary Assembly

    Range
    43773665..43776375 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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