Human Gene PCYT1B (uc004dbi.3) Description and Page Index
  Description: Homo sapiens phosphate cytidylyltransferase 1, choline, beta (PCYT1B), transcript variant 1, mRNA.
RefSeq Summary (NM_004845): The protein encoded by this gene belongs to the cytidylyltransferase family. It is involved in the regulation of phosphatidylcholine biosynthesis. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009].
Transcript (Including UTRs)
   Position: hg19 chrX:24,576,204-24,665,455 Size: 89,252 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chrX:24,580,410-24,665,222 Size: 84,813 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:24,576,204-24,665,455)mRNA (may differ from genome)Protein (369 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PCY1B_HUMAN
DESCRIPTION: RecName: Full=Choline-phosphate cytidylyltransferase B; EC=2.7.7.15; AltName: Full=CCT-beta; AltName: Full=CTP:phosphocholine cytidylyltransferase B; Short=CCT B; Short=CT B; AltName: Full=Phosphorylcholine transferase B;
FUNCTION: Controls phosphatidylcholine synthesis.
CATALYTIC ACTIVITY: CTP + phosphocholine = diphosphate + CDP- choline.
PATHWAY: Phospholipid metabolism; phosphatidylcholine biosynthesis; phosphatidylcholine from phosphocholine: step 1/2.
SUBCELLULAR LOCATION: Endoplasmic reticulum.
TISSUE SPECIFICITY: Highly expressed in testis, placenta, brain, ovary and fetus.
PTM: Extensively phosphorylated. The beta-1 isoform seems to be much less phosphorylated.
SIMILARITY: Belongs to the cytidylyltransferase family.
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/pcyt1b/";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PCYT1B
CDC HuGE Published Literature: PCYT1B

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.60 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 83.23 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -69.29233-0.297 Picture PostScript Text
3' UTR -1422.374206-0.338 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
IPR004821 - Cyt_trans-like
IPR004820 - Cytidylyltransf
IPR014729 - Rossmann-like_a/b/a_fold

Pfam Domains:
PF01467 - Cytidylyltransferase-like

SCOP Domains:
52374 - Nucleotidylyl transferase

ModBase Predicted Comparative 3D Structure on Q9Y5K3
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004105 choline-phosphate cytidylyltransferase activity
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity

Biological Process:
GO:0001541 ovarian follicle development
GO:0006629 lipid metabolic process
GO:0006656 phosphatidylcholine biosynthetic process
GO:0006657 CDP-choline pathway
GO:0007283 spermatogenesis
GO:0008654 phospholipid biosynthetic process
GO:0009058 biosynthetic process

Cellular Component:
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane


-  Descriptions from all associated GenBank mRNAs
  BC045634 - Homo sapiens phosphate cytidylyltransferase 1, choline, beta, mRNA (cDNA clone MGC:39750 IMAGE:5285137), complete cds.
AK226121 - Homo sapiens mRNA for PCYT1B protein variant, clone: hh13530.
AF148464 - Homo sapiens CTP:phosphocholine cytidylyltransferase CCTB2 isoform (PCYT1B) mRNA, complete cds.
AF052510 - Homo sapiens CTP:phosphocholine cytidylyltransferase b (CTB) mRNA, complete cds.
AK296333 - Homo sapiens cDNA FLJ50783 complete cds, highly similar to Choline-phosphate cytidylyltransferase B (EC2.7.7.15).
AK315323 - Homo sapiens cDNA, FLJ96359, Homo sapiens phosphate cytidylyltransferase 1, choline, betaisoform (PCYT1B), mRNA.
KJ898027 - Synthetic construct Homo sapiens clone ccsbBroadEn_07421 PCYT1B gene, encodes complete protein.
AK022741 - Homo sapiens cDNA FLJ12679 fis, clone NT2RM4002420.
JD342182 - Sequence 323206 from Patent EP1572962.
JD108096 - Sequence 89120 from Patent EP1572962.
JD218813 - Sequence 199837 from Patent EP1572962.
JD258672 - Sequence 239696 from Patent EP1572962.
JD320142 - Sequence 301166 from Patent EP1572962.
JD214699 - Sequence 195723 from Patent EP1572962.
JD492488 - Sequence 473512 from Patent EP1572962.
JD074395 - Sequence 55419 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00564 - Glycerophospholipid metabolism
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
PWY-3561 - choline biosynthesis III
PWY3O-450 - phosphatidylcholine biosynthesis I

Reactome (by CSHL, EBI, and GO)

Protein Q9Y5K3 (Reactome details) participates in the following event(s):

R-HSA-1483081 PCho and CTP are condensed to CDP-Cho by PCYT1 dimer
R-HSA-1483191 Synthesis of PC
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-1483257 Phospholipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A8IX00, B2RCX8, CCTB, NM_004845, NP_004836, O60621, PCY1B_HUMAN, Q86XC9, Q9Y5K3
UCSC ID: uc004dbi.3
RefSeq Accession: NM_004845
Protein: Q9Y5K3 (aka PCY1B_HUMAN or CTPU_HUMAN)
CCDS: CCDS14213.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004845.4
exon count: 8CDS single in 3' UTR: no RNA size: 5564
ORF size: 1110CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2405.00frame shift in genome: no % Coverage: 99.73
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 4356# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
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