Human Gene PPIB (uc002and.3) Description and Page Index
  Description: Homo sapiens peptidylprolyl isomerase B (cyclophilin B) (PPIB), mRNA.
RefSeq Summary (NM_000942): The protein encoded by this gene is a cyclosporine-binding protein and is mainly located within the endoplasmic reticulum. It is associated with the secretory pathway and released in biological fluids. This protein can bind to cells derived from T- and B-lymphocytes, and may regulate cyclosporine A-mediated immunosuppression. Variants have been identified in this protein that give rise to recessive forms of osteogenesis imperfecta. [provided by RefSeq, Oct 2009]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: EU794651.1, SRR1163658.412242.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968189, SAMEA1968540 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr15:64,448,014-64,455,354 Size: 7,341 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr15:64,448,222-64,455,185 Size: 6,964 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:64,448,014-64,455,354)mRNA (may differ from genome)Protein (216 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: PPIB_HUMAN
DESCRIPTION: RecName: Full=Peptidyl-prolyl cis-trans isomerase B; Short=PPIase B; EC=5.2.1.8; AltName: Full=CYP-S1; AltName: Full=Cyclophilin B; AltName: Full=Rotamase B; AltName: Full=S-cyclophilin; Short=SCYLP; Flags: Precursor;
FUNCTION: PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
CATALYTIC ACTIVITY: Peptidylproline (omega=180) = peptidylproline (omega=0).
ENZYME REGULATION: Cyclosporin A (CsA) inhibits CYPB.
SUBUNIT: Interacts with DYM.
SUBCELLULAR LOCATION: Endoplasmic reticulum lumen. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
DISEASE: Defects in PPIB are the cause of osteogenesis imperfecta type 9 (OI9) [MIM:259440]. OI9 is a connective tissue disorder characterized by bone fragility, low bone mass and bowing of limbs due to multiple fractures. Short limb dwarfism and blue sclerae are observed in some but not all patients.
SIMILARITY: Belongs to the cyclophilin-type PPIase family. PPIase B subfamily.
SIMILARITY: Contains 1 PPIase cyclophilin-type domain.
CAUTION: It is uncertain whether Met-1 or Met-9 is the initiator.
SEQUENCE CAUTION: Sequence=AAA52150.1; Type=Erroneous initiation;
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/ppib/";
WEB RESOURCE: Name=Osteogenesis imperfecta variant database; Note=Peptidyl-prolyl cis-trans isomerase B (PPIB); URL="http://oi.gene.le.ac.uk/home.php?select_db=PPIB";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PPIB
CDC HuGE Published Literature: PPIB

-  MalaCards Disease Associations
  MalaCards Gene Search: PPIB
Diseases sorted by gene-association score: osteogenesis imperfecta, type ix* (1218), ppib-related osteogenesis imperfecta* (200), osteogenesis imperfecta, type ii* (157), osteogenesis imperfecta, type iv* (117), osteogenesis imperfecta, type iii* (117), osteogenesis imperfecta (24), syphilis (6), bruck syndrome (5), connective tissue disease (2), bone development disease (1)
* = Manually curated disease association

-  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: 400.86 RPKM in Cells - Transformed fibroblasts
Total median expression: 7424.93 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 -79.02169-0.468 Picture PostScript Text
3' UTR -62.25208-0.299 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
IPR002130 - Cyclophilin-like_PPIase_dom
IPR024936 - Cyclophilin-type_PPIase
IPR020892 - Cyclophilin-type_PPIase_CS

Pfam Domains:
PF00160 - Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD

SCOP Domains:
50891 - Cyclophilin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1CYN
- X-ray MuPIT

3ICH
- X-ray MuPIT

3ICI
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P23284
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003755 peptidyl-prolyl cis-trans isomerase activity
GO:0005515 protein binding
GO:0016018 cyclosporin A binding
GO:0016853 isomerase activity
GO:0044877 macromolecular complex binding
GO:0051082 unfolded protein binding
GO:0070063 RNA polymerase binding
GO:0005518 collagen binding

Biological Process:
GO:0000413 protein peptidyl-prolyl isomerization
GO:0006457 protein folding
GO:0040018 positive regulation of multicellular organism growth
GO:0044794 positive regulation by host of viral process
GO:0044829 positive regulation by host of viral genome replication
GO:0050821 protein stabilization
GO:0060348 bone development
GO:0061077 chaperone-mediated protein folding
GO:1901873 regulation of post-translational protein modification

Cellular Component:
GO:0005634 nucleus
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0005790 smooth endoplasmic reticulum
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0032991 macromolecular complex
GO:0034663 endoplasmic reticulum chaperone complex
GO:0042470 melanosome
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF208545 - JP 2014500723-A/16048: Polycomb-Associated Non-Coding RNAs.
BC001125 - Homo sapiens peptidylprolyl isomerase B (cyclophilin B), mRNA (cDNA clone MGC:2224 IMAGE:2966791), complete cds.
M63573 - Human secreted cyclophilin-like protein (SCYLP) mRNA, complete cds.
EU794651 - Homo sapiens epididymis secretory protein Li 39 (HEL-S-39) mRNA, complete cds.
AK291149 - Homo sapiens cDNA FLJ76402 complete cds, highly similar to Homo sapiens peptidylprolyl isomerase B (cyclophilin B) (PPIB), mRNA.
BC032138 - Homo sapiens peptidylprolyl isomerase B (cyclophilin B), mRNA (cDNA clone MGC:29698 IMAGE:4896656), complete cds.
BC020800 - Homo sapiens peptidylprolyl isomerase B (cyclophilin B), mRNA (cDNA clone MGC:23783 IMAGE:4248828), complete cds.
U95646 - Homo sapiens drug resistance-associated protein (DRP), cyclophilin-like mRNA sequence.
M60857 - Human cyclophilin B (hCyPB) mRNA, complete cds.
BC008848 - Homo sapiens peptidylprolyl isomerase B (cyclophilin B), mRNA (cDNA clone MGC:14109 IMAGE:3502055), complete cds.
M60457 - Human cyclophilin mRNA, 3' end.
JD119581 - Sequence 100605 from Patent EP1572962.
LF377513 - JP 2014500723-A/185016: Polycomb-Associated Non-Coding RNAs.
JD324986 - Sequence 306010 from Patent EP1572962.
JD439407 - Sequence 420431 from Patent EP1572962.
JD336694 - Sequence 317718 from Patent EP1572962.
JD527302 - Sequence 508326 from Patent EP1572962.
JD291504 - Sequence 272528 from Patent EP1572962.
JD077021 - Sequence 58045 from Patent EP1572962.
JD565034 - Sequence 546058 from Patent EP1572962.
KJ897363 - Synthetic construct Homo sapiens clone ccsbBroadEn_06757 PPIB gene, encodes complete protein.
DQ892289 - Synthetic construct clone IMAGE:100004919; FLH184906.01X; RZPDo839D02146D peptidylprolyl isomerase B (cyclophilin B) (PPIB) gene, encodes complete protein.
DQ895488 - Synthetic construct Homo sapiens clone IMAGE:100009948; FLH184902.01L; RZPDo839D02145D peptidylprolyl isomerase B (cyclophilin B) (PPIB) gene, encodes complete protein.
AB528494 - Synthetic construct DNA, clone: pF1KB6971, Homo sapiens PPIB gene for peptidylprolyl isomerase B, without stop codon, in Flexi system.
CR456829 - Homo sapiens full open reading frame cDNA clone RZPDo834F0415D for gene PPIB, peptidylprolyl isomerase B (cyclophilin B); complete cds, incl. stopcodon.
LF377512 - JP 2014500723-A/185015: Polycomb-Associated Non-Coding RNAs.
LF377511 - JP 2014500723-A/185014: Polycomb-Associated Non-Coding RNAs.
CU679145 - Synthetic construct Homo sapiens gateway clone IMAGE:100020201 5' read PPIB mRNA.
FZ437619 - JP 2006507841-A/29: Functional and Hyperfunctional siRNA.
JD020497 - Sequence 1521 from Patent EP1572962.
JD030060 - Sequence 11084 from Patent EP1572962.
AK311074 - Homo sapiens cDNA, FLJ18116.
D28465 - Homo sapiens mRNA for peptidyl-prolyl cis-trans isomerase B, 5'UTR region.
JD406497 - Sequence 387521 from Patent EP1572962.
JD161353 - Sequence 142377 from Patent EP1572962.
JD395006 - Sequence 376030 from Patent EP1572962.
JD478859 - Sequence 459883 from Patent EP1572962.
JD140254 - Sequence 121278 from Patent EP1572962.
MA444122 - JP 2018138019-A/16048: Polycomb-Associated Non-Coding RNAs.
MA613090 - JP 2018138019-A/185016: Polycomb-Associated Non-Coding RNAs.
MA613089 - JP 2018138019-A/185015: Polycomb-Associated Non-Coding RNAs.
MA613088 - JP 2018138019-A/185014: Polycomb-Associated Non-Coding RNAs.

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

Protein P23284 (Reactome details) participates in the following event(s):

R-HSA-2022073 Procollagen triple helix formation
R-HSA-8948230 P3HB binds 4-Hyp-collagen propeptides
R-HSA-1980233 Collagen prolyl 3-hydroxylase converts 4-Hyp collagen to 3,4-Hyp collagen
R-HSA-1650814 Collagen biosynthesis and modifying enzymes
R-HSA-1474290 Collagen formation
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: A8K534, CYPB, NM_000942, NP_000933, P23284, PPIB_HUMAN, Q6IBH5, Q9BVK5
UCSC ID: uc002and.3
RefSeq Accession: NM_000942
Protein: P23284 (aka PPIB_HUMAN)
CCDS: CCDS10191.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000942.4
exon count: 5CDS single in 3' UTR: no RNA size: 1045
ORF size: 651CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1442.00frame shift in genome: no % Coverage: 98.37
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.