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    Tpcn2 two pore segment channel 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309139, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Tpcn2provided by RGD
    Official Full Name
    two pore segment channel 2provided by RGD
    Primary source
    RGD:1311779
    See related
    EnsemblRapid:ENSRNOG00000013387 AllianceGenome:RGD:1311779
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable several functions, including identical protein binding activity; monoatomic cation channel activity; and phosphatidylinositol-3,5-bisphosphate binding activity. Involved in response to vitamin D. Predicted to be located in endolysosome membrane and melanosome membrane. Predicted to be active in lysosomal membrane. Biomarker of brain infarction. Human ortholog(s) of this gene implicated in pigmentation disease. Orthologous to human TPCN2 (two pore segment channel 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Liver (RPKM 40.4), Thymus (RPKM 38.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tpcn2 in Genome Data Viewer
    Location:
    1q42
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (209845827..209875561, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (200416538..200446252, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (218419182..218448902, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120099969 Neighboring gene small integral membrane protein 38 Neighboring gene MAS related GPR family member F Neighboring gene MAS related GPR family member D

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Suppression subtractive hybridization analysis of low-protein diet- and vitamin D-induced gene expression from rat kidney inner medullary base. Chen G, et al. Physiol Genomics, 2010 May. PMID 20197420, Free PMC Article
    2. NAADP-induced intracellular calcium ion is mediated by the TPCs (two-pore channels) in hypoxia-induced pulmonary arterial hypertension. Hu W, et al. J Cell Mol Med, 2021 Aug. PMID 34263977, Free PMC Article
    3. TPC2 proteins mediate nicotinic acid adenine dinucleotide phosphate (NAADP)- and agonist-evoked contractions of smooth muscle. Tugba Durlu-Kandilci N, et al. J Biol Chem, 2010 Aug 6. PMID 20547763, Free PMC Article
    4. Identification of a novel gene for diabetic traits in rats, mice, and humans. Tsaih SW, et al. Genetics, 2014 Sep. PMID 25236446, Free PMC Article
    5. Characterization of two-pore channel 2 (TPCN2)-mediated Ca2+ currents in isolated lysosomes. Schieder M, et al. J Biol Chem, 2010 Jul 9. PMID 20495006, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NAADP-induced intracellular calcium ion is mediated by the TPCs (two-pore channels) in hypoxia-induced pulmonary arterial hypertension.
      Title: NAADP-induced intracellular calcium ion is mediated by the TPCs (two-pore channels) in hypoxia-induced pulmonary arterial hypertension.
    2. Tpcn2 was identified as a novel gene for diabetic traits in rats.
      Title: Identification of a novel gene for diabetic traits in rats, mice, and humans.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    NOT enables NAADP-sensitive calcium-release channel activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables NAADP-sensitive calcium-release channel activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables calcium channel activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ligand-gated sodium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ligand-gated sodium channel activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol-3,5-bisphosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT enables voltage-gated calcium channel activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables voltage-gated calcium channel activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT enables voltage-gated sodium channel activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcium-mediated signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in calcium-mediated signaling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endocytosis involved in viral entry into host cell IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endocytosis involved in viral entry into host cell ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endosome to lysosome transport of low-density lipoprotein particle ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in intracellular calcium ion homeostasis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in intracellular pH reduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lysosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of developmental pigmentation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in receptor-mediated endocytosis of virus by host cell IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of exocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in release of sequestered calcium ion into cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to vitamin D IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in smooth muscle contraction ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sodium ion transmembrane transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endolysosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in melanosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    two pore channel protein 2
    Names
    two pore calcium channel protein 2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001399445.1 → NP_001386374.1  two pore channel protein 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the protein-coding transcript.
      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A6HYJ3, D3ZTJ6, F1MAS6
      Conserved Domains (1) summary
      pfam00520
      Location:413 → 678
      Ion_trans; Ion transport protein

    RNA

    1. NR_174187.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      209845827..209875561 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039079208.2 → XP_038935136.1  two pore channel protein 2 isoform X2

      UniProtKB/TrEMBL
      A6HYJ3, D3ZTJ6
      Conserved Domains (1) summary
      pfam00520
      Location:66 → 297
      Ion_trans; Ion transport protein

    2. XM_039079203.2 → XP_038935131.1  two pore channel protein 2 isoform X1

      UniProtKB/TrEMBL
      A6HYJ3, D3ZTJ6
      Conserved Domains (1) summary
      pfam00520
      Location:66 → 297
      Ion_trans; Ion transport protein

    3. XM_039079211.2 → XP_038935139.1  two pore channel protein 2 isoform X3

      UniProtKB/TrEMBL
      A6HYJ3, D3ZTJ6
      Related
      ENSRNOP00000051739.3, ENSRNOT00000054857.6
      Conserved Domains (1) summary
      pfam00520
      Location:66 → 297
      Ion_trans; Ion transport protein

    4. XM_063264183.1 → XP_063120253.1  two pore channel protein 2 isoform X4

    5. XM_039079228.2 → XP_038935156.1  two pore channel protein 2 isoform X5

      Conserved Domains (1) summary
      pfam00520
      Location:478 → 629
      Ion_trans; Ion transport protein

    6. XM_039079253.2 → XP_038935181.1  two pore channel protein 2 isoform X8

      Conserved Domains (1) summary
      pfam00520
      Location:312 → 463
      Ion_trans; Ion transport protein

    7. XM_039079267.2 → XP_038935195.1  two pore channel protein 2 isoform X10

      Conserved Domains (1) summary
      pfam00520
      Location:64 → 329
      Ion_trans; Ion transport protein

    8. XM_063264189.1 → XP_063120259.1  two pore channel protein 2 isoform X6

    9. XM_039079244.2 → XP_038935172.1  two pore channel protein 2 isoform X7

      UniProtKB/TrEMBL
      B2RYH7
      Conserved Domains (1) summary
      pfam00520
      Location:66 → 297
      Ion_trans; Ion transport protein

    10. XM_039079256.2 → XP_038935184.1  two pore channel protein 2 isoform X9

      UniProtKB/TrEMBL
      B2RYH7
      Conserved Domains (1) summary
      pfam00520
      Location:66 → 297
      Ion_trans; Ion transport protein

    RNA

    1. XR_010053038.1 RNA Sequence

    2. XR_005486642.2 RNA Sequence

    3. XR_005486643.2 RNA Sequence

    4. XR_005486644.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107566.1: Suppressed sequence

      Description
      NM_001107566.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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