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    PCYT1B phosphate cytidylyltransferase 1B, choline [ Homo sapiens (human) ]

    Gene ID: 9468, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PCYT1Bprovided by HGNC
    Official Full Name
    phosphate cytidylyltransferase 1B, cholineprovided by HGNC
    Primary source
    HGNC:HGNC:8755
    See related
    Ensembl:ENSG00000102230 MIM:300948; AllianceGenome:HGNC:8755
    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
    CTB; CCTB
    Summary
    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]
    Expression
    Biased expression in brain (RPKM 6.6), testis (RPKM 2.8) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PCYT1B in Genome Data Viewer
    Location:
    Xp22.11
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (24558087..24672887, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (24142375..24257164, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (24576204..24691004, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S26 pseudogene 58 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20719 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:24509351-24510314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29505 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:24546061-24546668 Neighboring gene pyruvate dehydrogenase kinase 3 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:24546669-24547275 Neighboring gene SNRPE pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29506 Neighboring gene uncharacterized LOC124905262 Neighboring gene PCYT1B antisense RNA 1 Neighboring gene ribosomal protein L23 pseudogene Neighboring gene H2B histone pseudogene 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:24710004-24710504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29507 Neighboring gene DNA polymerase alpha 1, catalytic subunit Neighboring gene small Cajal body-specific RNA 23

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Cloning and characterization of a second human CTP:phosphocholine cytidylyltransferase. Lykidis A, et al. J Biol Chem, 1998 May 29. PMID 9593753
    2. Mass spectrometric identification of human phosphate cytidylyltransferase 1 as a novel calcium oxalate crystal growth inhibitor purified from human renal stone matrix. Priyadarshini, et al. Clin Chim Acta, 2009 Oct. PMID 19595683
    3. Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets. Yue L, et al. Mol Biol Cell, 2020 May 1. PMID 32186954, Free PMC Article
    4. CTP:phosphocholine cytidylyltransferase: Function, regulation, and structure of an amphitropic enzyme required for membrane biogenesis. Cornell RB, et al. Prog Lipid Res, 2015 Jul. PMID 26165797
    5. Neurokinin 3 receptor and phosphocholine transferase: missing factors for pathogenesis of C-reactive protein in preeclampsia. Parchim NF, et al. Hypertension, 2015 Feb. PMID 25452470, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets.
      Title: Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets.
    2. Genetic Polymorphisms of LPCAT1, CHPT1 and PCYT1B and Risk of Neonatal Respiratory Distress Syndrome among a Chinese Han Population.
      Title: Genetic Polymorphisms of LPCAT1, CHPT1 and PCYT1B and Risk of Neonatal Respiratory Distress Syndrome among a Chinese Han Population.
    3. CCT contributes to phospholipid compositional homeostasis. [Review]
      Title: CTP:phosphocholine cytidylyltransferase: Function, regulation, and structure of an amphitropic enzyme required for membrane biogenesis.
    4. PCYT1B, a placental-specific enzyme post-translationally modifying neurokinin B, is essential for the pathogenic role of CRP in preeclampsia through activation of the neurokinin 3 receptor.
      Title: Neurokinin 3 receptor and phosphocholine transferase: missing factors for pathogenesis of C-reactive protein in preeclampsia.
    5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    7. Human phosphate cytidylyltransferase 1, choline, beta is a novel CaOx crystal growth inhibitor.
      Title: Mass spectrometric identification of human phosphate cytidylyltransferase 1 as a novel calcium oxalate crystal growth inhibitor purified from human renal stone matrix.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables choline-phosphate cytidylyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables choline-phosphate cytidylyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables phosphatidylcholine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in CDP-choline pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ovarian follicle development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylcholine biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    choline-phosphate cytidylyltransferase B
    Names
    CCT B
    CCT-beta
    CT B
    CTP:phosphocholine cytidylyltransferase b
    CTP:phosphocholine cytidylyltransferase-beta
    choline-phosphate cytidylyltransferase beta
    phosphate cytidylyltransferase 1, choline, beta
    phosphorylcholine transferase B
    phosphorylcholine transferase beta
    NP_001156736.1
    NP_001156737.1
    NP_004836.2
    XP_016885466.1
    XP_054184152.1

    NCBI Reference Sequences (RefSeq)

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    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_013253.1 RefSeqGene

      Range
      30516..119776
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001163264.2 → NP_001156736.1  choline-phosphate cytidylyltransferase B isoform 2

      See identical proteins and their annotated locations for NP_001156736.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon compared to variant 1. This results in the use of a different start codon, and a shorter isoform (2) with a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC079168, AK226121, BC045634
      Consensus CDS
      CCDS55392.1
      UniProtKB/Swiss-Prot
      Q9Y5K3
      Related
      ENSP00000368440.1, ENST00000379145.5
      Conserved Domains (1) summary
      PLN02413
      Location:54 → 296
      PLN02413; choline-phosphate cytidylyltransferase

    2. NM_001163265.2 → NP_001156737.1  choline-phosphate cytidylyltransferase B isoform 3

      See identical proteins and their annotated locations for NP_001156737.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) is alternatively spliced at the 3' end compared to variant 1, resulting in a frameshift and a shorter isoform (3) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC079168, AF052510, AK226121, AK315323, BC045634
      Consensus CDS
      CCDS55391.1
      UniProtKB/Swiss-Prot
      Q9Y5K3
      Related
      ENSP00000349211.4, ENST00000356768.8
      Conserved Domains (1) summary
      cd02174
      Location:75 → 224
      CCT; CTP:phosphocholine cytidylyltransferase

    3. NM_004845.5 → NP_004836.2  choline-phosphate cytidylyltransferase B isoform 1

      See identical proteins and their annotated locations for NP_004836.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1.
      Source sequence(s)
      AC079168, AK226121, AK315323, BC045634
      Consensus CDS
      CCDS14213.1
      UniProtKB/Swiss-Prot
      A8IX00, B2RCX8, B4DK10, E9PD84, O60621, Q86XC9, Q9Y5K3
      Related
      ENSP00000368439.2, ENST00000379144.7
      Conserved Domains (1) summary
      PLN02413
      Location:72 → 314
      PLN02413; choline-phosphate cytidylyltransferase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      24558087..24672887 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017029977.2 → XP_016885466.1  choline-phosphate cytidylyltransferase B isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      24142375..24257164 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328177.1 → XP_054184152.1  choline-phosphate cytidylyltransferase B isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5K3.1 GenPept UniProtKB/Swiss-Prot:Q9Y5K3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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