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

Gene ID: 309139, updated on 27-Nov-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, Nov 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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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
    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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