Human Gene TPCN1 (uc001tux.3) Description and Page Index
  Description: Homo sapiens two pore segment channel 1 (TPCN1), transcript variant 1, mRNA.
RefSeq Summary (NM_001143819): Voltage-gated Ca(2+) and Na+ channels have 4 homologous domains, each containing 6 transmembrane segments, S1 to S6. TPCN1 is similar to these channels, but it has only 2 domains containing S1 to S6 (Ishibashi et al., 2000 [PubMed 10753632]).[supplied by OMIM, Mar 2008].
Transcript (Including UTRs)
   Position: hg19 chr12:113,659,260-113,736,389 Size: 77,130 Total Exon Count: 29 Strand: +
Coding Region
   Position: hg19 chr12:113,663,051-113,733,881 Size: 70,831 Coding Exon Count: 28 

Page IndexSequence and LinksMalaCardsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:113,659,260-113,736,389)mRNA (may differ from genome)Protein (888 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  MalaCards Disease Associations
  MalaCards Gene Search: TPCN1
Diseases sorted by gene-association score: endocrine gland cancer (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 69.31 RPKM in Brain - Cerebellum
Total median expression: 1123.59 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -97.10174-0.558 Picture PostScript Text
3' UTR -1043.442508-0.416 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
  Pfam Domains:
PF00520 - Ion transport protein

SCOP Domains:
81324 - Voltage-gated potassium channels

ModBase Predicted Comparative 3D Structure on Q9ULQ1-3
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK093490 - Homo sapiens cDNA FLJ36171 fis, clone TESTI2026215, highly similar to Homo sapiens two pore segment channel 1 (TPCN1), mRNA.
AX748162 - Sequence 1687 from Patent EP1308459.
AY083666 - Homo sapiens two-pore channel 1 (TPC1) mRNA, complete cds.
AB032995 - Homo sapiens KIAA1169 mRNA for KIAA1169 protein.
BC152423 - Homo sapiens two pore segment channel 1, mRNA (cDNA clone MGC:176656 IMAGE:8862535), complete cds.
JD081327 - Sequence 62351 from Patent EP1572962.
JD271133 - Sequence 252157 from Patent EP1572962.
BC136795 - Homo sapiens two pore segment channel 1, mRNA (cDNA clone MGC:168408 IMAGE:9020785), complete cds.
BC136796 - Homo sapiens two pore segment channel 1, mRNA (cDNA clone MGC:168409 IMAGE:9020786), complete cds.
BC142664 - Homo sapiens two pore segment channel 1, mRNA (cDNA clone MGC:164911 IMAGE:40148126), complete cds.
AK057414 - Homo sapiens cDNA FLJ32852 fis, clone TESTI2003454, highly similar to Rattus norvegicus mRNA for voltage-gated ca channel.
BC150203 - Homo sapiens two pore segment channel 1, mRNA (cDNA clone MGC:165054 IMAGE:40148827), complete cds.
JD212207 - Sequence 193231 from Patent EP1572962.
JD412393 - Sequence 393417 from Patent EP1572962.
JD412151 - Sequence 393175 from Patent EP1572962.
AB384128 - Synthetic construct DNA, clone: pF1KSDA1169, Homo sapiens TPCN1 gene for two-pore calcium channel protein 1, complete cds, without stop codon, in Flexi system.
KJ893995 - Synthetic construct Homo sapiens clone ccsbBroadEn_03389 TPCN1 gene, encodes complete protein.
AK296268 - Homo sapiens cDNA FLJ54008 complete cds, highly similar to Homo sapiens two pore segment channel 1 (TPCN1), mRNA.
AK295022 - Homo sapiens cDNA FLJ54674 complete cds, highly similar to Homo sapiens two pore segment channel 1 (TPCN1), mRNA.
AK075071 - Homo sapiens cDNA FLJ90590 fis, clone PLACE1001016, weakly similar to SODIUM CHANNEL PROTEIN PARA.
BC069234 - Homo sapiens cDNA clone IMAGE:5090822, partial cds.
BC007419 - Homo sapiens two pore segment channel 1, mRNA (cDNA clone IMAGE:3010316), partial cds.
JD064852 - Sequence 45876 from Patent EP1572962.
JD127432 - Sequence 108456 from Patent EP1572962.
JD565856 - Sequence 546880 from Patent EP1572962.
JD485833 - Sequence 466857 from Patent EP1572962.
JD217620 - Sequence 198644 from Patent EP1572962.
BC110885 - Homo sapiens cDNA clone IMAGE:5762420.
AK025838 - Homo sapiens cDNA: FLJ22185 fis, clone HRC00988.
AK000619 - Homo sapiens cDNA FLJ20612 fis, clone KAT05509.
BC068001 - Homo sapiens cDNA clone IMAGE:6026044, partial cds.
JD365939 - Sequence 346963 from Patent EP1572962.
BC098423 - Homo sapiens signal sequence receptor, delta (translocon-associated protein delta), mRNA (cDNA clone IMAGE:6262290), **** WARNING: chimeric clone ****.
JD389363 - Sequence 370387 from Patent EP1572962.
JD443139 - Sequence 424163 from Patent EP1572962.
JD054688 - Sequence 35712 from Patent EP1572962.
JD477066 - Sequence 458090 from Patent EP1572962.
JD384738 - Sequence 365762 from Patent EP1572962.
JD488966 - Sequence 469990 from Patent EP1572962.
JD320768 - Sequence 301792 from Patent EP1572962.
JD060553 - Sequence 41577 from Patent EP1572962.
JD362987 - Sequence 344011 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9ULQ1 (Reactome details) participates in the following event(s):

R-HSA-2685505 TPCN1/2 transport lysosomal Ca2+ to cytosol
R-HSA-2672351 Stimuli-sensing channels
R-HSA-983712 Ion channel transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA1169, NM_001143819, NP_060371, Q9ULQ1-3, TPC1
UCSC ID: uc001tux.3
RefSeq Accession: NM_001143819
Protein: Q9ULQ1-3, splice isoform of Q9ULQ1 CCDS: CCDS44985.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001143819.1
exon count: 29CDS single in 3' UTR: no RNA size: 5472
ORF size: 2667CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5534.00frame shift in genome: no % Coverage: 97.75
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.