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Field

Term
Gene name

Class

Subclass

Chromosome

External id

In atlas

Reliability

Reliability

Reliability

Validation

Method

Validation

Method

Validation

Method

Validation

Location

Searches

Tissue

Cell type

Expression

Tissue

Specificity

Cell line

Specificity

Cancer

Specificity

Tissue

Detectable

Cell line

Detectable

Cancer

Detectable

Cancer

Prognosis

Category

Score

Score

Score

Antibodies

Column

 
 
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TPCN1
  • TISSUE

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PATHOLOGY ATLAS

GENE/PROTEIN

Antibody validation

Dictionary

Level of antibody staining/expression





High
Medium
Low
Not detected

GENERAL INFORMATION

Gene namei

Gene name according to HGNC.

TPCN1

Gene descriptioni

Gene description according to HGNC.

Two pore segment channel 1

Protein classi

Protein class the gene product belongs to according to selected gene lists. List of protein classes.

Predicted intracellular proteins
Predicted membrane proteins
Transporters
Voltage-gated ion channels

Predicted localizationi

Protein localization predicted from several bioinformatic algorithms.

Read more

Intracellular,Membrane

Number of transcriptsi

Number of protein-coding transcribed from this gene as defined by Ensembl.

15
SHOW MORE

HUMAN PROTEIN ATLAS INFORMATION

RNA categoryi

RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue/cell line enriched, group enriched, tissue/cell line enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for The Cancer Genome Atlas (TCGA) data from cancer tissues and internally generated Human Protein Atlas (HPA) data from normal tissues and cell lines.

TCGA (cancer tissue):Expressed in all
HPA (cell line):Expressed in all
HPA (normal tissue):Expressed in all

Protein evidencei

Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.

Evidence at protein level

Protein expression
normal tissuei

A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation.

"Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile.

Read more

Cytoplasmic expression in several tissues.

ANTIBODY IHC RELIABILITY

Data reliability
descriptioni

Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.

Antibody staining mainly consistent with RNA expression data.

Reliability scorei

Reliability score (score description), divided into Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between the staining pattern of one antibody or several antibodies with RNA-seq data and available gene/protein characterization data.

Read more

Approved based on 1 antibody.
HPA039757
SHOW MORE

PROGNOSTIC SUMMARYi

Kaplan-Meier plots for all cancers where high expression of this gene has significant (p<0.001) association with patient survival are shown in this summary. Whether the prognosis is favourable or unfavourable is indicated in brackets. Each Kaplan-Meier plot is clickable and redirects to a detailed page that includes individual expression and survival data for patients with the selected cancer.

Gene product is not prognostic.
Show all

RNA EXPRESSION OVERVIEWi

RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).

TCGA dataseti
RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. To access cancer specific RNA and prognostic data, click on the cancer name.

Read more
RNA cancer category: Expressed in all

PROTEIN EXPRESSIONi

Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.

For histological reference, visit the histological dictionary.

Colorectal cancer
Breast cancer
Prostate cancer
Lung cancer
Liver cancer

STAINING SUMMARYi

For each cancer, the fraction of samples with protein expression level high, medium, low, or not detected are provided by the blue-scale color-coding (as described by the color-coding scale in the box to the left). The length of the bar represents the number of patient samples analyzed (max=12 patients). The images and annotations can be accessed by clicking on the cancer name or protein expression bar. If more than one antibody is analyzed, the tabs at the top of the staining summary section can be used to toggle between the different antibodies. The mouse-over function displays additional data for the features in the staining summary view.

Next to the cancer staining data, the protein expression data of normal tissues or specific cell types corresponding to each cancer are shown and protein expression levels are indicated by the blue-scale color coding.

HPA039757

Cancer

Cancer staining

Protein
expression of
normal tissue

Breast cancer
 
Carcinoid
 
Cervical cancer
 
 
Colorectal cancer
 
 
Endometrial cancer
 
 
Glioma
 
Head and neck cancer
 
 
Liver cancer
 
 
Lung cancer
 
Lymphoma
 
 

Cancer

Cancer staining

Protein
expression of
normal tissue

Melanoma
 
Ovarian cancer
 
Pancreatic cancer
 
Prostate cancer
 
Renal cancer
 
Skin cancer
 
Stomach cancer
 
 
Testis cancer
 
Thyroid cancer
 
Urothelial cancer
 

Staining summaryi

A manually written summary of the overall protein expression pattern across the analyzed cancer tissues.

Several case of malignant melanomas, breast, prostate, testicular, pancreatic, liver and colorectal cancers showed weak to moderate cytoplasmic staining. Other malignant cells were in general negative.

GENE INFORMATIONi

Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.

Gene name

TPCN1 (HGNC Symbol)

Synonyms

FLJ20612, KIAA1169, TPC1

Description

Two pore segment channel 1 (HGNC Symbol)

Entrez gene summary

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]

Chromosome

12

Cytoband

q24.13

Chromosome location (bp)

113221050 - 113298585

Protein evidence

Evidence at protein level (all genes)

Ensembl

ENSG00000186815 (version 83.38)

Entrez gene

53373

UniProt

Q9ULQ1 (UniProt - Evidence at protein level)

neXtProt

NX_Q9ULQ1

Antibodypedia

TPCN1 antibodies

PROTEIN BROWSERi

The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.

At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.

Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50) (read more).

If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.

Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.

«
TPCN1-001
TPCN1-002
TPCN1-003
TPCN1-011
TPCN1-013
TPCN1-014
TPCN1-015
TPCN1-016
TPCN1-017
TPCN1-018
TPCN1-019
TPCN1-020
TPCN1-021
TPCN1-022
TPCN1-201
»

PROTEIN INFORMATIONi

The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.

The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.

The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.

The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.

Splice variant

UniProt

Protein class

Gene ontology

Length & mass

Signal peptide
(predicted)

Transmembrane regions
(predicted)

TPCN1-001
ENSP00000335300
ENST00000335509
Q9ULQ1 [Direct mapping]
Two pore calcium channel protein 1
Show all
Transporters
   Transporter channels and pores
Voltage-gated ion channels
   CatSper and Two-Pore Channels
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   >9TM proteins predicted by MDM
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005216 [ion channel activity]
GO:0005245 [voltage-gated calcium channel activity]
GO:0005515 [protein binding]
GO:0005765 [lysosomal membrane]
GO:0005886 [plasma membrane]
GO:0006811 [ion transport]
GO:0006816 [calcium ion transport]
GO:0010008 [endosome membrane]
GO:0016020 [membrane]
GO:0016021 [integral component of membrane]
GO:0034220 [ion transmembrane transport]
GO:0034765 [regulation of ion transmembrane transport]
GO:0042802 [identical protein binding]
GO:0055085 [transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0072345 [NAADP-sensitive calcium-release channel activity]
GO:0086010 [membrane depolarization during action potential]
Show all
816 aa
94.1 kDa
No >9
TPCN1-002
ENSP00000448083
ENST00000550785
Q9ULQ1 [Direct mapping]
Two pore calcium channel protein 1
Show all
Transporters
   Transporter channels and pores
Voltage-gated ion channels
   CatSper and Two-Pore Channels
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   >9TM proteins predicted by MDM
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005216 [ion channel activity]
GO:0005245 [voltage-gated calcium channel activity]
GO:0005515 [protein binding]
GO:0005765 [lysosomal membrane]
GO:0005886 [plasma membrane]
GO:0006811 [ion transport]
GO:0006816 [calcium ion transport]
GO:0010008 [endosome membrane]
GO:0016020 [membrane]
GO:0016021 [integral component of membrane]
GO:0034220 [ion transmembrane transport]
GO:0034765 [regulation of ion transmembrane transport]
GO:0042802 [identical protein binding]
GO:0055085 [transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0072345 [NAADP-sensitive calcium-release channel activity]
GO:0086010 [membrane depolarization during action potential]
Show all
888 aa
101.8 kDa
No >9
TPCN1-003
ENSP00000376350
ENST00000392569
B7Z3R2 [Direct mapping]
Two pore calcium channel protein 1; cDNA FLJ54008, highly similar to Homo sapiens two pore segment channel 1 (TPCN1), mRNA
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   >9TM proteins predicted by MDM
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005216 [ion channel activity]
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006811 [ion transport]
GO:0006816 [calcium ion transport]
GO:0016020 [membrane]
GO:0016021 [integral component of membrane]
GO:0034220 [ion transmembrane transport]
GO:0034765 [regulation of ion transmembrane transport]
GO:0055085 [transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
748 aa
87.3 kDa
No >9
TPCN1-011
ENSP00000449564
ENST00000546781
H0YIK4 [Direct mapping]
Two pore calcium channel protein 1
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   2TM proteins predicted by MDM
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005216 [ion channel activity]
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006811 [ion transport]
GO:0006816 [calcium ion transport]
GO:0016020 [membrane]
GO:0016021 [integral component of membrane]
GO:0034220 [ion transmembrane transport]
GO:0034765 [regulation of ion transmembrane transport]
GO:0055085 [transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
204 aa
23.8 kDa
No 2
TPCN1-013
ENSP00000448561
ENST00000548465
F8VR74 [Direct mapping]
Two pore calcium channel protein 1
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   3TM proteins predicted by MDM
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006816 [calcium ion transport]
GO:0016021 [integral component of membrane]
GO:0034220 [ion transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
145 aa
16.7 kDa
No 3
TPCN1-014
ENSP00000448704
ENST00000549279
F8W0K7 [Direct mapping]
Two pore calcium channel protein 1
Show all
Predicted intracellular proteins
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006816 [calcium ion transport]
GO:0034220 [ion transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
100 aa
10.7 kDa
No 0
TPCN1-015
ENSP00000449560
ENST00000547275
F8VVY9 [Direct mapping]
Two pore calcium channel protein 1
Show all
Predicted intracellular proteins
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006816 [calcium ion transport]
GO:0034220 [ion transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
147 aa
15.7 kDa
No 0
TPCN1-016
ENSP00000447569
ENST00000552985
F8W0P9 [Direct mapping]
Two pore calcium channel protein 1
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   # TM segments-based
   1TM proteins predicted by MDM
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006816 [calcium ion transport]
GO:0034220 [ion transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
215 aa
22.9 kDa
No 1
TPCN1-017
ENSP00000447806
ENST00000552642
F8VS97 [Direct mapping]
Two pore calcium channel protein 1
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   # TM segments-based
   1TM proteins predicted by MDM
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006816 [calcium ion transport]
GO:0034220 [ion transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
126 aa
13.7 kDa
No 1
TPCN1-018
ENSP00000447073
ENST00000550873
F8W1G4 [Direct mapping]
Two pore calcium channel protein 1
Show all
Predicted intracellular proteins
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006816 [calcium ion transport]
GO:0034220 [ion transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
85 aa
8.8 kDa
No 0
TPCN1-019
ENSP00000447263
ENST00000551096
F8VZZ6 [Direct mapping]
Two pore calcium channel protein 1
Show all
   SPOCTOPUS predicted secreted proteins
Predicted intracellular proteins
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006816 [calcium ion transport]
GO:0034220 [ion transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
124 aa
12.9 kDa
No 0
TPCN1-020
ENSP00000447181
ENST00000551099
F8W0K7 [Direct mapping]
Two pore calcium channel protein 1
Show all
Predicted intracellular proteins
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006816 [calcium ion transport]
GO:0034220 [ion transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
100 aa
10.7 kDa
No 0
TPCN1-021
ENSP00000449944
ENST00000552897
F8VV93 [Direct mapping]
Two pore calcium channel protein 1
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   2TM proteins predicted by MDM
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006816 [calcium ion transport]
GO:0016021 [integral component of membrane]
GO:0034220 [ion transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
107 aa
12.3 kDa
No 2
TPCN1-022
ENSP00000446767
ENST00000552542
F8W1L6 [Direct mapping]
Two pore calcium channel protein 1
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   2TM proteins predicted by MDM
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005245 [voltage-gated calcium channel activity]
GO:0005886 [plasma membrane]
GO:0006816 [calcium ion transport]
GO:0016021 [integral component of membrane]
GO:0034220 [ion transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0086010 [membrane depolarization during action potential]
Show all
120 aa
13.7 kDa
No 2
TPCN1-201
ENSP00000438125
ENST00000541517
Q9ULQ1 [Direct mapping]
Two pore calcium channel protein 1
Show all
Transporters
   Transporter channels and pores
Voltage-gated ion channels
   CatSper and Two-Pore Channels
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   >9TM proteins predicted by MDM
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005216 [ion channel activity]
GO:0005245 [voltage-gated calcium channel activity]
GO:0005515 [protein binding]
GO:0005765 [lysosomal membrane]
GO:0005886 [plasma membrane]
GO:0006811 [ion transport]
GO:0006816 [calcium ion transport]
GO:0010008 [endosome membrane]
GO:0016020 [membrane]
GO:0016021 [integral component of membrane]
GO:0034220 [ion transmembrane transport]
GO:0034765 [regulation of ion transmembrane transport]
GO:0042802 [identical protein binding]
GO:0055085 [transmembrane transport]
GO:0070588 [calcium ion transmembrane transport]
GO:0072345 [NAADP-sensitive calcium-release channel activity]
GO:0086010 [membrane depolarization during action potential]
Show all
888 aa
101.8 kDa
No >9

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