Human Gene PCM1 (uc003wyi.4) Description and Page Index
  Description: Homo sapiens pericentriolar material 1 (PCM1), mRNA.
RefSeq Summary (NM_006197): The protein encoded by this gene is a component of centriolar satellites, which are electron dense granules scattered around centrosomes. Inhibition studies show that this protein is essential for the correct localization of several centrosomal proteins, and for anchoring microtubules to the centrosome. Chromosomal aberrations involving this gene are associated with papillary thyroid carcinomas and a variety of hematological malignancies, including atypical chronic myeloid leukemia and T-cell lymphoma. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015].
Transcript (Including UTRs)
   Position: hg19 chr8:17,780,366-17,887,457 Size: 107,092 Total Exon Count: 39 Strand: +
Coding Region
   Position: hg19 chr8:17,793,120-17,885,171 Size: 92,052 Coding Exon Count: 37 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:17,780,366-17,887,457)mRNA (may differ from genome)Protein (2024 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
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OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: PCM1_HUMAN
DESCRIPTION: RecName: Full=Pericentriolar material 1 protein; Short=PCM-1; Short=hPCM-1;
FUNCTION: Required for centrosome assembly and function. Essential for the correct localization of several centrosomal proteins including CEP250, CETN3, PCNT and NEK2. Required to anchor microtubules to the centrosome. Involved in the biogenesis of cilia.
SUBUNIT: Self-associates (By similarity). Interacts with BBS4, BBS8, CETN3, HAP1, NDE1 and NDEL1.
INTERACTION: Q8NFJ9:BBS1; NbExp=2; IntAct=EBI-741421, EBI-1805484; Q96RK4:BBS4; NbExp=16; IntAct=EBI-741421, EBI-1805814;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton. Cytoplasm, cytoskeleton, centrosome. Cytoplasmic granule. Note=Localizes to cytoplasmic granules which are enriched around the centrosome. This centrosomal enrichment requires microtubules and dynein. The majority of the protein dissociates from the centrosome during metaphase and subsequently localizes to the cleavage site in telophase.
TISSUE SPECIFICITY: Expressed in blood, bone marrow, breast, lymph node, ovary and thyroid.
INDUCTION: Expression is reduced in breast and ovarian cancer.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Defects in PCM1 are a cause of thyroid papillary carcinoma (TPC) [MIM:188550]. TPC is a common tumor of the thyroid that typically arises as an irregular, solid or cystic mass from otherwise normal thyroid tissue. Papillary carcinomas are malignant neoplasm characterized by the formation of numerous, irregular, finger-like projections of fibrous stroma that is covered with a surface layer of neoplastic epithelial cells. Note=A chromosomal aberration involving PCM1 is found in thyroid papillary carcinomas. Translocation t(8;10)(p21.3;q11.2) with RET links the protein kinase domain of RET to the major portion of PCM1.
DISEASE: Note=A chromosomal aberration involving PCM1 is found in a variety of hematological malignancies including atypical chronic myeloid leukemia (atypical CML) and T-cell lymphoma. Translocation t(8;9)(p22;p24) with JAK2 links the protein kinase domain of JAK2 to the major portion of PCM1.
SIMILARITY: Belongs to the PCM1 family.
SEQUENCE CAUTION: Sequence=AAH27477.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH65022.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAC03656.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAC14882.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PCM1
CDC HuGE Published Literature: PCM1
Positive Disease Associations: schizophrenia
Related Studies:
  1. schizophrenia
    Gurling, H. M. et al. 2006, Genetic Association and Brain Morphology Studies and the Chromosome 8p22 Pericentriolar Material 1 (PCM1) Gene in Susceptibility to Schizophrenia, Arch Gen Psychiatry 2006 63(8) 844-854. [PubMed 16894060]
    The PCM1 gene is implicated in susceptibility to schizophrenia and is associated with orbitofrontal gray matter volumetric deficits.

-  MalaCards Disease Associations
  MalaCards Gene Search: PCM1
Diseases sorted by gene-association score: differentiated thyroid carcinoma* (143), atypical chronic myeloid leukemia (17), occult macular dystrophy (11), bardet-biedl syndrome 4 (10), bardet-biedl syndrome (2)
* = 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: 59.65 RPKM in Testis
Total median expression: 805.66 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 -188.01422-0.446 Picture PostScript Text
3' UTR -572.242286-0.250 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
IPR024138 - Pericentriolar_Pcm1

Pfam Domains:
PF15717 - Pericentriolar material 1 C terminus

ModBase Predicted Comparative 3D Structure on Q15154
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0042802 identical protein binding

Biological Process:
GO:0000086 G2/M transition of mitotic cell cycle
GO:0001764 neuron migration
GO:0007098 centrosome cycle
GO:0010389 regulation of G2/M transition of mitotic cell cycle
GO:0022027 interkinetic nuclear migration
GO:0030030 cell projection organization
GO:0031122 cytoplasmic microtubule organization
GO:0034453 microtubule anchoring
GO:0034454 microtubule anchoring at centrosome
GO:0035176 social behavior
GO:0035735 intraciliary transport involved in cilium assembly
GO:0050768 negative regulation of neurogenesis
GO:0060271 cilium assembly
GO:0071539 protein localization to centrosome
GO:0090316 positive regulation of intracellular protein transport
GO:0097150 neuronal stem cell population maintenance
GO:0097711 ciliary basal body docking
GO:1905515 non-motile cilium assembly

Cellular Component:
GO:0000242 pericentriolar material
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005814 centriole
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0016020 membrane
GO:0031965 nuclear membrane
GO:0032991 macromolecular complex
GO:0034451 centriolar satellite
GO:0035869 ciliary transition zone
GO:0036064 ciliary basal body
GO:0042995 cell projection
GO:0045177 apical part of cell
GO:0097730 non-motile cilium


-  Descriptions from all associated GenBank mRNAs
  L27841 - Human autoantigen pericentriol material 1 (PCM-1) mRNA, complete cds.
LF384362 - JP 2014500723-A/191865: Polycomb-Associated Non-Coding RNAs.
BC140946 - Homo sapiens pericentriolar material 1, mRNA (cDNA clone MGC:176623 IMAGE:9056758), complete cds.
BC133052 - Homo sapiens pericentriolar material 1, mRNA (cDNA clone MGC:144935 IMAGE:8381608), complete cds.
AB587340 - Synthetic construct DNA, clone: pF1KB9485, Homo sapiens PCM1 gene for pericentriolar material 1, without stop codon, in Flexi system.
AX785390 - Sequence 1 from Patent WO03050301.
AF068293 - Homo sapiens HDCMB07P mRNA, partial cds.
MA619939 - JP 2018138019-A/191865: Polycomb-Associated Non-Coding RNAs.
BC098391 - Homo sapiens cDNA clone IMAGE:30334722.
AK307583 - Homo sapiens cDNA, FLJ97531.
BC000453 - Homo sapiens pericentriolar material 1, mRNA (cDNA clone IMAGE:2821465), complete cds.
BC065022 - Homo sapiens pericentriolar material 1, mRNA (cDNA clone IMAGE:6046257), partial cds.
BC027477 - Homo sapiens pericentriolar material 1, mRNA (cDNA clone IMAGE:3905908), partial cds.
LF372130 - JP 2014500723-A/179633: Polycomb-Associated Non-Coding RNAs.
JD416974 - Sequence 397998 from Patent EP1572962.
JD257755 - Sequence 238779 from Patent EP1572962.
JD465659 - Sequence 446683 from Patent EP1572962.
JD530658 - Sequence 511682 from Patent EP1572962.
JD549356 - Sequence 530380 from Patent EP1572962.
LF372135 - JP 2014500723-A/179638: Polycomb-Associated Non-Coding RNAs.
CU674224 - Synthetic construct Homo sapiens gateway clone IMAGE:100017689 5' read PCM1 mRNA.
KJ901626 - Synthetic construct Homo sapiens clone ccsbBroadEn_11020 PCM1 gene, encodes complete protein.
LF372136 - JP 2014500723-A/179639: Polycomb-Associated Non-Coding RNAs.
LF372138 - JP 2014500723-A/179641: Polycomb-Associated Non-Coding RNAs.
LF372139 - JP 2014500723-A/179642: Polycomb-Associated Non-Coding RNAs.
LF372144 - JP 2014500723-A/179647: Polycomb-Associated Non-Coding RNAs.
LF372146 - JP 2014500723-A/179649: Polycomb-Associated Non-Coding RNAs.
LF372147 - JP 2014500723-A/179650: Polycomb-Associated Non-Coding RNAs.
LF372148 - JP 2014500723-A/179651: Polycomb-Associated Non-Coding RNAs.
LF372150 - JP 2014500723-A/179653: Polycomb-Associated Non-Coding RNAs.
LF372151 - JP 2014500723-A/179654: Polycomb-Associated Non-Coding RNAs.
LF372153 - JP 2014500723-A/179656: Polycomb-Associated Non-Coding RNAs.
LF372155 - JP 2014500723-A/179658: Polycomb-Associated Non-Coding RNAs.
LF372156 - JP 2014500723-A/179659: Polycomb-Associated Non-Coding RNAs.
LF372161 - JP 2014500723-A/179664: Polycomb-Associated Non-Coding RNAs.
LF372162 - JP 2014500723-A/179665: Polycomb-Associated Non-Coding RNAs.
LF372163 - JP 2014500723-A/179666: Polycomb-Associated Non-Coding RNAs.
MA607707 - JP 2018138019-A/179633: Polycomb-Associated Non-Coding RNAs.
MA607712 - JP 2018138019-A/179638: Polycomb-Associated Non-Coding RNAs.
MA607713 - JP 2018138019-A/179639: Polycomb-Associated Non-Coding RNAs.
MA607715 - JP 2018138019-A/179641: Polycomb-Associated Non-Coding RNAs.
MA607716 - JP 2018138019-A/179642: Polycomb-Associated Non-Coding RNAs.
MA607721 - JP 2018138019-A/179647: Polycomb-Associated Non-Coding RNAs.
MA607723 - JP 2018138019-A/179649: Polycomb-Associated Non-Coding RNAs.
MA607724 - JP 2018138019-A/179650: Polycomb-Associated Non-Coding RNAs.
MA607725 - JP 2018138019-A/179651: Polycomb-Associated Non-Coding RNAs.
MA607727 - JP 2018138019-A/179653: Polycomb-Associated Non-Coding RNAs.
MA607728 - JP 2018138019-A/179654: Polycomb-Associated Non-Coding RNAs.
MA607730 - JP 2018138019-A/179656: Polycomb-Associated Non-Coding RNAs.
MA607732 - JP 2018138019-A/179658: Polycomb-Associated Non-Coding RNAs.
MA607733 - JP 2018138019-A/179659: Polycomb-Associated Non-Coding RNAs.
MA607738 - JP 2018138019-A/179664: Polycomb-Associated Non-Coding RNAs.
MA607739 - JP 2018138019-A/179665: Polycomb-Associated Non-Coding RNAs.
MA607740 - JP 2018138019-A/179666: Polycomb-Associated Non-Coding RNAs.
AK295856 - Homo sapiens cDNA FLJ56445 complete cds, highly similar to Homo sapiens pericentriolar material 1 (PCM1), mRNA.
LF372165 - JP 2014500723-A/179668: Polycomb-Associated Non-Coding RNAs.
AK091406 - Homo sapiens cDNA FLJ34087 fis, clone FCBBF3005330, highly similar to Human autoantigen pericentriol material 1 (PCM-1) mRNA.
AX746961 - Sequence 486 from Patent EP1308459.
LF372166 - JP 2014500723-A/179669: Polycomb-Associated Non-Coding RNAs.
AK302378 - Homo sapiens cDNA FLJ54972 complete cds, highly similar to Homo sapiens pericentriolar material 1 (PCM1), mRNA.
AK301727 - Homo sapiens cDNA FLJ53611 complete cds, highly similar to Homo sapiens pericentriolar material 1 (PCM1), mRNA.
AJ297349 - Homo sapiens t(8;10)(p21.3;q11.2) translocation breakpoint for partial RET/PCM-1 fusion gene.
LF372171 - JP 2014500723-A/179674: Polycomb-Associated Non-Coding RNAs.
LF372172 - JP 2014500723-A/179675: Polycomb-Associated Non-Coding RNAs.
LF372173 - JP 2014500723-A/179676: Polycomb-Associated Non-Coding RNAs.
LF372174 - JP 2014500723-A/179677: Polycomb-Associated Non-Coding RNAs.
LF372175 - JP 2014500723-A/179678: Polycomb-Associated Non-Coding RNAs.
LF372176 - JP 2014500723-A/179679: Polycomb-Associated Non-Coding RNAs.
LF372177 - JP 2014500723-A/179680: Polycomb-Associated Non-Coding RNAs.
LF372178 - JP 2014500723-A/179681: Polycomb-Associated Non-Coding RNAs.
LF372179 - JP 2014500723-A/179682: Polycomb-Associated Non-Coding RNAs.
LF372180 - JP 2014500723-A/179683: Polycomb-Associated Non-Coding RNAs.
LF372181 - JP 2014500723-A/179684: Polycomb-Associated Non-Coding RNAs.
JD090248 - Sequence 71272 from Patent EP1572962.
LF372182 - JP 2014500723-A/179685: Polycomb-Associated Non-Coding RNAs.
JD179066 - Sequence 160090 from Patent EP1572962.
JD179067 - Sequence 160091 from Patent EP1572962.
MA607742 - JP 2018138019-A/179668: Polycomb-Associated Non-Coding RNAs.
MA607743 - JP 2018138019-A/179669: Polycomb-Associated Non-Coding RNAs.
MA607748 - JP 2018138019-A/179674: Polycomb-Associated Non-Coding RNAs.
MA607749 - JP 2018138019-A/179675: Polycomb-Associated Non-Coding RNAs.
MA607750 - JP 2018138019-A/179676: Polycomb-Associated Non-Coding RNAs.
MA607751 - JP 2018138019-A/179677: Polycomb-Associated Non-Coding RNAs.
MA607752 - JP 2018138019-A/179678: Polycomb-Associated Non-Coding RNAs.
MA607753 - JP 2018138019-A/179679: Polycomb-Associated Non-Coding RNAs.
MA607754 - JP 2018138019-A/179680: Polycomb-Associated Non-Coding RNAs.
MA607755 - JP 2018138019-A/179681: Polycomb-Associated Non-Coding RNAs.
MA607756 - JP 2018138019-A/179682: Polycomb-Associated Non-Coding RNAs.
MA607757 - JP 2018138019-A/179683: Polycomb-Associated Non-Coding RNAs.
MA607758 - JP 2018138019-A/179684: Polycomb-Associated Non-Coding RNAs.
MA607759 - JP 2018138019-A/179685: Polycomb-Associated Non-Coding RNAs.

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

Protein Q15154 (Reactome details) participates in the following event(s):

R-HSA-380272 Plk1-mediated phosphorylation of Nlp
R-HSA-380283 Recruitment of additional gamma tubulin/ gamma TuRC to the centrosome
R-HSA-380294 Loss of C-Nap-1 from centrosomes
R-HSA-380311 Recruitment of Plk1 to centrosomes
R-HSA-380455 Recruitment of CDK11p58 to the centrosomes
R-HSA-380303 Dissociation of Phospho-Nlp from the centrosome
R-HSA-5626220 C2CD3 binds the mother centriole
R-HSA-380508 Translocation of NuMA to the centrosomes
R-HSA-2574845 AJUBA binds centrosome-associated AURKA
R-HSA-8853405 TPX2 binds AURKA at centrosomes
R-HSA-3000319 BORA binds PLK1 and AURKA
R-HSA-2574840 AJUBA facilitates AURKA autophosphorylation
R-HSA-3000310 AURKA phosphorylates PLK1
R-HSA-5626223 C2CD3 and OFD1 recruit 5 distal appendage proteins to the centriole
R-HSA-5626681 Recruitment of transition zone proteins
R-HSA-5626227 CP110 and CEP97 dissociate from the centriole
R-HSA-380316 Association of NuMA with microtubules
R-HSA-8853419 TPX2 promotes AURKA autophosphorylation
R-HSA-5626228 The distal appendage proteins recruit TTBK2
R-HSA-5638009 CEP164 recruits RAB3IP-carrying Golgi-derived vesicles to the basal body
R-HSA-5626699 MARK4 binds ODF2 in the centriole
R-HSA-5617816 RAB3IP stimulates nucleotide exchange on RAB8A
R-HSA-380259 Loss of Nlp from mitotic centrosomes
R-HSA-380270 Recruitment of mitotic centrosome proteins and complexes
R-HSA-380284 Loss of proteins required for interphase microtubule organization from the centrosome
R-HSA-5620912 Anchoring of the basal body to the plasma membrane
R-HSA-380320 Recruitment of NuMA to mitotic centrosomes
R-HSA-2565942 Regulation of PLK1 Activity at G2/M Transition
R-HSA-8854518 AURKA Activation by TPX2
R-HSA-380287 Centrosome maturation
R-HSA-5617833 Cilium Assembly
R-HSA-68877 Mitotic Prometaphase
R-HSA-69275 G2/M Transition
R-HSA-1852241 Organelle biogenesis and maintenance
R-HSA-68886 M Phase
R-HSA-453274 Mitotic G2-G2/M phases
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: NM_006197, NP_006188, PCM1_HUMAN, Q15154, Q58F13, Q6P1K7, Q8NB85, Q9BWC1, Q9H4A2
UCSC ID: uc003wyi.4
RefSeq Accession: NM_006197
Protein: Q15154 (aka PCM1_HUMAN)
CCDS: CCDS47812.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006197.3
exon count: 39CDS single in 3' UTR: no RNA size: 8788
ORF size: 6075CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 12276.50frame shift in genome: no % Coverage: 99.94
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.