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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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SLC52A3
  • 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.

SLC52A3

Gene descriptioni

Gene description according to HGNC.

Solute carrier family 52 (riboflavin transporter), member 3

Protein classi

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

Disease related genes
Plasma proteins
Potential drug targets
Predicted membrane proteins
Transporters

Predicted localizationi

Protein localization predicted from several bioinformatic algorithms.

Read more

Membrane

Number of transcriptsi

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

3
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):Cell line enhanced (CAPAN-2, SK-BR-3, T-47d)
HPA (normal tissue):Tissue enhanced (testis)

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 different tissue types, most abundant in testis.

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. Pending external verification.

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.
HPA049391
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.

Prognostic marker in stomach cancer (favourable).
Stomach cancer p<0.001
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.

HPA049391

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.

Most of the cancer tissues displayed weak to moderate cytoplasmic positivity. A few cases of squamous cell carcinomas were strongly stained. Malignant lymphomas, testis, renal and stomach cancers were 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

SLC52A3 (HGNC Symbol)

Synonyms

bA371L19.1, C20orf54, hRFT2, RFVT3

Description

Solute carrier family 52 (riboflavin transporter), member 3 (HGNC Symbol)

Entrez gene summary

This gene encodes a riboflavin transporter protein that is strongly expressed in the intestine and likely plays a role in intestinal absorption of riboflavin. The protein is predicted to have eleven transmembrane domains and a cell surface localization signal in the C-terminus. Mutations at this locus have been associated with Brown-Vialetto-Van Laere syndrome and Fazio-Londe disease. [provided by RefSeq, Mar 2012]

Chromosome

20

Cytoband

p13

Chromosome location (bp)

760080 - 776015

Protein evidence

Evidence at protein level (all genes)

Ensembl

ENSG00000101276 (version 83.38)

Entrez gene

113278

UniProt

Q9NQ40 (UniProt - Evidence at protein level)

neXtProt

NX_Q9NQ40

Antibodypedia

SLC52A3 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.

SLC52A3-001
SLC52A3-004
SLC52A3-201

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)

SLC52A3-001
ENSP00000217254
ENST00000217254
Q9NQ40 [Direct mapping]
Solute carrier family 52, riboflavin transporter, member 3
K0A6P4 [Target identity:100%; Query identity:100%]
Chromosome 20 open reading frame 54, isoform CRA_c; Solute carrier family 52 member 3
Show all
Transporters
   Electrochemical Potential-driven transporters
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
Plasma proteins
Disease related genes
Potential drug targets
Show all
GO:0005886 [plasma membrane]
GO:0005887 [integral component of plasma membrane]
GO:0006766 [vitamin metabolic process]
GO:0006767 [water-soluble vitamin metabolic process]
GO:0006771 [riboflavin metabolic process]
GO:0007605 [sensory perception of sound]
GO:0016324 [apical plasma membrane]
GO:0032217 [riboflavin transporter activity]
GO:0032218 [riboflavin transport]
GO:0044281 [small molecule metabolic process]
Show all
469 aa
50.8 kDa
Yes >9
SLC52A3-004
ENSP00000371370
ENST00000381944
Q9NQ40 [Direct mapping]
Solute carrier family 52, riboflavin transporter, member 3
Show all
Transporters
   Electrochemical Potential-driven transporters
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
   8TM proteins predicted by MDM
Plasma proteins
Disease related genes
Potential drug targets
Show all
GO:0005886 [plasma membrane]
GO:0005887 [integral component of plasma membrane]
GO:0006766 [vitamin metabolic process]
GO:0006767 [water-soluble vitamin metabolic process]
GO:0006771 [riboflavin metabolic process]
GO:0007605 [sensory perception of sound]
GO:0016324 [apical plasma membrane]
GO:0032217 [riboflavin transporter activity]
GO:0032218 [riboflavin transport]
GO:0044281 [small molecule metabolic process]
Show all
415 aa
45 kDa
Yes 8
SLC52A3-201
ENSP00000488723
ENST00000632431
Q9NQ40 [Direct mapping]
Solute carrier family 52, riboflavin transporter, member 3
K0A6P4 [Target identity:100%; Query identity:100%]
Chromosome 20 open reading frame 54, isoform CRA_c; Solute carrier family 52 member 3
Show all
Transporters
   Electrochemical Potential-driven transporters
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
Plasma proteins
Disease related genes
Potential drug targets
Protein evidence (Kim et al 2014)
Show all
GO:0005515 [protein binding]
GO:0005886 [plasma membrane]
GO:0005887 [integral component of plasma membrane]
GO:0006766 [vitamin metabolic process]
GO:0006767 [water-soluble vitamin metabolic process]
GO:0006771 [riboflavin metabolic process]
GO:0007605 [sensory perception of sound]
GO:0016324 [apical plasma membrane]
GO:0032217 [riboflavin transporter activity]
GO:0032218 [riboflavin transport]
GO:0034605 [cellular response to heat]
GO:0044281 [small molecule metabolic process]
Show all
469 aa
50.8 kDa
No >9

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The Human Protein Atlas project is funded
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