Tpcn1 two pore segment channel 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tpcn1provided by RGD
Official Full Name: two pore segment channel 1provided by RGD
Primary source: RGD:708494
See related: Ensembl:ENSRNOG00000059344 AllianceGenome:RGD:708494
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 cation channel activity; phosphatidylinositol-3,5-bisphosphate binding activity; and protein homodimerization activity. Predicted to be involved in endocytosis involved in viral entry into host cell; positive regulation of autophagy; and sodium ion transmembrane transport. Predicted to be located in early endosome membrane; endolysosome; and recycling endosome membrane. Predicted to be integral component of membrane. Predicted to be active in endosome membrane and lysosomal membrane. Orthologous to human TPCN1 (two pore segment channel 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 363.8), Muscle (RPKM 181.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 12q16

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	12	NC_086030.1 (41633399..41690200)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	12	NC_051347.1 (35972813..36029632)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	12	NC_005111.4 (41507784..41566847)

Chromosome 12 - NC_086030.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
TPC1 is involved in the norepinephrine (NE)-stimulated [Ca(2+)]i rise in Smooth muscle cells. Inhibition of TPC1 activity by NED 19 could be the reason for partial inhibition of aortic rings contraction in response to NE.
Title: The Role of Two-Pore Channels in Norepinephrine-Induced [Ca(2+)](i) Rise in Rat Aortic Smooth Muscle Cells and Aorta Contraction.
Rat GnRH neurones express all five subtypes of voltage-gated Ca(2+) channels and exhibit an apamin-sensitive I(sAHP), which may allow continuous firing in response to a relatively strong depolarizing input.
Title: The SK channel blocker apamin inhibits slow afterhyperpolarization currents in rat gonadotropin-releasing hormone neurones.

Submit: New GeneRIF Correction

General gene information

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Markers

RH130280 (e-PCR)
- UniSTS:213567

RH131571 (e-PCR)
- UniSTS:214854

D12Got83 (e-PCR)
- UniSTS:115057

Tpcn1 (e-PCR), detects polymorphism
- UniSTS:536693

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables NAADP-sensitive calcium-release channel activity	IEA Inferred from Electronic Annotation more info
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
NOT enables NAADP-sensitive calcium-release channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity	IEA Inferred from Electronic Annotation more info
enables intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity	ISO Inferred from Sequence Orthology more info
enables intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables ligand-gated sodium channel activity	IEA Inferred from Electronic Annotation more info
enables ligand-gated sodium channel activity	ISO Inferred from Sequence Orthology more info
enables ligand-gated sodium channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables monoatomic ion channel activity	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol-3,5-bisphosphate binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol-3,5-bisphosphate binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables syntaxin binding	IEA Inferred from Electronic Annotation more info
enables syntaxin binding	ISO Inferred from Sequence Orthology more info
enables voltage-gated channel activity	IEA Inferred from Electronic Annotation more info
enables voltage-gated sodium channel activity	IEA Inferred from Electronic Annotation more info
enables voltage-gated sodium channel activity	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in calcium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in calcium-mediated signaling	IEA Inferred from Electronic Annotation more info
involved_in endocytosis involved in viral entry into host cell	IEA Inferred from Electronic Annotation more info
involved_in endocytosis involved in viral entry into host cell	ISO Inferred from Sequence Orthology more info
involved_in monoatomic ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of autophagy	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transmembrane transport	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
located_in early endosome membrane	ISO Inferred from Sequence Orthology more info
located_in early endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in endolysosome	IEA Inferred from Electronic Annotation more info
located_in endolysosome	ISO Inferred from Sequence Orthology more info
located_in endolysosome	ISS Inferred from Sequence or Structural Similarity more info
is_active_in endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome membrane	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	ISO Inferred from Sequence Orthology more info
part_of monoatomic ion channel complex	IEA Inferred from Electronic Annotation more info
located_in recycling endosome membrane	IEA Inferred from Electronic Annotation more info
located_in recycling endosome membrane	ISO Inferred from Sequence Orthology more info
located_in recycling endosome membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: two pore calcium channel protein 1

Names: two pore channel 1; voltage-dependent calcium channel protein TPC1; voltage-gated Ca channel

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)

NM_139332.3 → NP_647548.2 two pore calcium channel protein 1

Status: VALIDATED

Source sequence(s)

AB018253, BC062072, CA339864, CK473123, JAXUCZ010000012

UniProtKB/Swiss-Prot

Q6P6R1, Q9WTN5

UniProtKB/TrEMBL

A0A0G2K2X9

Related

ENSRNOP00000072420.2, ENSRNOT00000083890.2

Conserved Domains (1) summary

pfam00520
Location:441 → 692

Ion_trans; Ion transport protein

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

NC_086030.1 Reference GRCr8

Range

41633399..41690200

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039089065.2 → XP_038944993.1 two pore calcium channel protein 1 isoform X2

UniProtKB/Swiss-Prot

Q6P6R1, Q9WTN5

Conserved Domains (1) summary

pfam00520
Location:434 → 685

Ion_trans; Ion transport protein
XM_039089067.2 → XP_038944995.1 two pore calcium channel protein 1 isoform X4

Conserved Domains (1) summary

pfam00520
Location:137 → 331

Ion_trans; Ion transport protein
XM_039089064.2 → XP_038944992.1 two pore calcium channel protein 1 isoform X1

UniProtKB/Swiss-Prot

Q6P6R1, Q9WTN5

UniProtKB/TrEMBL

A0A0G2K2X9

Conserved Domains (1) summary

pfam00520
Location:441 → 692

Ion_trans; Ion transport protein
XM_063271044.1 → XP_063127114.1 two pore calcium channel protein 1 isoform X1

UniProtKB/TrEMBL

A0A0G2K2X9
XM_039089066.2 → XP_038944994.1 two pore calcium channel protein 1 isoform X3

UniProtKB/Swiss-Prot

Q6P6R1, Q9WTN5

Conserved Domains (1) summary

pfam00520
Location:430 → 681

Ion_trans; Ion transport protein