Human Gene TPCN2 (uc009ysk.1) Description and Page Index
  Description: Homo sapiens two pore segment channel 2 (TPCN2), mRNA.
RefSeq Summary (NM_139075): This gene encodes a putative cation-selective ion channel with two repeats of a six-transmembrane-domain. The protein localizes to lysosomal membranes and enables nicotinic acid adenine dinucleotide phosphate (NAADP) -induced calcium ion release from lysosome-related stores. This ubiquitously expressed gene has elevated expression in liver and kidney. Two common nonsynonymous SNPs in this gene strongly associate with blond versus brown hair pigmentation.[provided by RefSeq, Dec 2009]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data because no single transcript was available for the full length of the gene. The extent of this transcript is supported by transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AY029200.1, BC063008.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000294309.8/ ENSP00000294309.3 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:68,816,350-68,846,261 Size: 29,912 Total Exon Count: 14 Strand: +


Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionOther SpeciesmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:68,816,350-68,846,261)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneNetworkH-INVHGNC
LynxPubMedStanford SOURCETreefamWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TPCN2
CDC HuGE Published Literature: TPCN2
Positive Disease Associations: Blond vs brown hair color , Cholesterol , Hair Color , Prostatic Neoplasms
Related Studies:
  1. Blond vs brown hair color
    Sulem ,et al. 2008, Two newly identified genetic determinants of pigmentation in Europeans, Nature genetics 2008 40- 7 : 835-7. [PubMed 18488028]
  2. Cholesterol
    , , . [PubMed 0]
  3. Hair Color
    Patrick Sulem et al. Nature genetics 2008, Two newly identified genetic determinants of pigmentation in Europeans., Nature genetics. [PubMed 18488028]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TPCN2
Diseases sorted by gene-association score: deafness, autosomal recessive 63 (12), deafness, autosomal recessive 7 (7), prostate cancer susceptibility (4)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.23 RPKM in Esophagus - Gastroesophageal Junction
Total median expression: 306.99 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.

-  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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK023366 - Homo sapiens cDNA FLJ13304 fis, clone OVARC1001391, highly similar to Homo sapiens two pore segment channel 2 (TPCN2), mRNA.
AY029200 - Homo sapiens two-pore calcium channel protein 2 mRNA, complete cds.
AK123089 - Homo sapiens cDNA FLJ41094 fis, clone ASTRO2014923.
BC063008 - Homo sapiens two pore segment channel 2, mRNA (cDNA clone MGC:70581 IMAGE:5214862), complete cds.
AK298919 - Homo sapiens cDNA FLJ58483 complete cds, highly similar to Homo sapiens two pore segment channel 2 (TPCN2), mRNA.
KJ900457 - Synthetic construct Homo sapiens clone ccsbBroadEn_09851 TPCN2 gene, encodes complete protein.
AB209253 - Homo sapiens mRNA for two pore segment channel 2 variant protein.
AL137479 - Homo sapiens mRNA; cDNA DKFZp434M0223 (from clone DKFZp434M0223); partial cds.
DQ587449 - Homo sapiens piRNA piR-54561, complete sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: AK023366
UCSC ID: uc009ysk.1
RefSeq Accession: NM_139075

-  Gene Model Information
 
category: nearCoding nonsense-mediated-decay: yes RNA accession: AK023366.1
exon count: 14CDS single in 3' UTR: no RNA size: 2200
ORF size: 0CDS single in intron: no Alignment % ID: 99.73
txCdsPredict score: 1258.00frame shift in genome: no % Coverage: 63.68
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.