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Aliases for SLC13A5 Gene

Aliases for SLC13A5 Gene

  • Solute Carrier Family 13 Member 5 2 3 5
  • Solute Carrier Family 13 (Sodium-Dependent Citrate Transporter), Member 5 2 3
  • Na(+)/Citrate Cotransporter 3 4
  • NaCT 3 4
  • Sodium-Dependent Dicarboxylate Transporter 3
  • Na+-Coupled Citrate Transporter Protein 3
  • Sodium-Dependent Citrate Transporter 4
  • Sodium-Coupled Citrate Transporter 4
  • EIEE25 3
  • MIndy 3
  • INDY 3

External Ids for SLC13A5 Gene

Previous GeneCards Identifiers for SLC13A5 Gene

  • GC17M006532
  • GC17M006788
  • GC17M006529
  • GC17M006588
  • GC17M006483

Summaries for SLC13A5 Gene

Entrez Gene Summary for SLC13A5 Gene

  • This gene encodes a protein belonging to the solute carrier family 13 group of proteins. This family member is a sodium-dependent citrate cotransporter that may regulate metabolic processes. Mutations in this gene cause early infantile epileptic encephalopathy 25. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]

GeneCards Summary for SLC13A5 Gene

SLC13A5 (Solute Carrier Family 13 Member 5) is a Protein Coding gene. Diseases associated with SLC13A5 include Epileptic Encephalopathy, Early Infantile, 25 and Epilepsy, Pyridoxine-Dependent. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. Gene Ontology (GO) annotations related to this gene include transporter activity and citrate transmembrane transporter activity. An important paralog of this gene is SLC13A2.

UniProtKB/Swiss-Prot for SLC13A5 Gene

  • High-affinity sodium/citrate cotransporter that mediates citrate entry into cells. The transport process is electrogenic; it is the trivalent form of citrate rather than the divalent form that is recognized as a substrate. May facilitate the utilization of circulating citrate for the generation of metabolic energy and for the synthesis of fatty acids and cholesterol.

Additional gene information for SLC13A5 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC13A5 Gene

Genomics for SLC13A5 Gene

GeneHancer (GH) Regulatory Elements for SLC13A5 Gene

Promoters and enhancers for SLC13A5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I006710 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE 583.9 +1.0 1047 3.8 FOXA2 ARID4B YBX1 ZNF48 YY1 TCF12 SLC30A9 GLIS2 ZNF207 ATF7 SLC13A5 ASGR1 ASGR2 DVL2 SNORD10 LOC100996842 SNORA48 WRAP53 SLC16A13 SLC16A11
GH17I006853 Promoter/Enhancer 1.6 Ensembl ENCODE 10.3 -141.1 -141094 2.7 ELF3 ARID4B SIN3A DMAP1 ZBTB7B THRB ZBTB40 RAD21 YY1 ETS1 ALOX12P2 TEKT1 FBXO39 BCL6B SLC13A5 MIR195 GC17M006868
GH17I006668 Enhancer 0.7 ENCODE 22.9 +43.2 43238 3.2 ELF3 SOX13 SAP130 NFIB KLF17 THRB ZNF48 RARA SOX5 NFIA GC17P006673 PIR54331 SLC13A5 TXNDC17 KIAA0753 FBXO39 TEKT1 BCL6B ENSG00000261996 CTDNEP1
GH17I006660 Enhancer 0.9 Ensembl dbSUPER 11 +52.6 52566 1.6 HDGF BMI1 BATF ZFHX2 POLR2A ATF7 ETV6 ZNF600 IKZF2 RUNX3 ENSG00000261996 TXNDC17 SLC13A5 PITPNM3 BCL6B TNK1 ENSG00000274114 ALOX15P1 C17orf100 PIR54331
GH17I006548 Enhancer 1 Ensembl ENCODE dbSUPER 9.6 +164.7 164658 1.3 PKNOX1 ZNF449 EBF1 ZIC2 ZFHX2 IKZF1 GLIS1 CREB1 EGR2 SLC13A5 KIAA0753 PITPNM3 GC17M006460 GC17P006525
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLC13A5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC13A5 gene promoter:

Genomic Locations for SLC13A5 Gene

Genomic Locations for SLC13A5 Gene
chr17:6,684,713-6,713,567
(GRCh38/hg38)
Size:
28,855 bases
Orientation:
Minus strand
chr17:6,588,032-6,616,886
(GRCh37/hg19)

Genomic View for SLC13A5 Gene

Genes around SLC13A5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC13A5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC13A5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC13A5 Gene

Proteins for SLC13A5 Gene

  • Protein details for SLC13A5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86YT5-S13A5_HUMAN
    Recommended name:
    Solute carrier family 13 member 5
    Protein Accession:
    Q86YT5
    Secondary Accessions:
    • B3KXR0
    • B7Z4P2
    • B7ZLB4
    • F8W7N2
    • Q6ZMG1

    Protein attributes for SLC13A5 Gene

    Size:
    568 amino acids
    Molecular mass:
    63062 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC13A5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC13A5 Gene

Post-translational modifications for SLC13A5 Gene

  • Glycosylation at isoforms=2, 3, 4562

No data available for DME Specific Peptides for SLC13A5 Gene

Domains & Families for SLC13A5 Gene

Gene Families for SLC13A5 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC13A5 Gene

Graphical View of Domain Structure for InterPro Entry

Q86YT5

UniProtKB/Swiss-Prot:

S13A5_HUMAN :
  • Belongs to the SLC13A/DASS transporter (TC 2.A.47) family. NADC subfamily.
Family:
  • Belongs to the SLC13A/DASS transporter (TC 2.A.47) family. NADC subfamily.
genes like me logo Genes that share domains with SLC13A5: view

Function for SLC13A5 Gene

Molecular function for SLC13A5 Gene

UniProtKB/Swiss-Prot Function:
High-affinity sodium/citrate cotransporter that mediates citrate entry into cells. The transport process is electrogenic; it is the trivalent form of citrate rather than the divalent form that is recognized as a substrate. May facilitate the utilization of circulating citrate for the generation of metabolic energy and for the synthesis of fatty acids and cholesterol.

Phenotypes From GWAS Catalog for SLC13A5 Gene

Gene Ontology (GO) - Molecular Function for SLC13A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015137 citrate transmembrane transporter activity TAS --
GO:0015141 succinate transmembrane transporter activity IBA --
GO:0015142 tricarboxylic acid transmembrane transporter activity IEA --
GO:0015293 symporter activity IEA --
GO:0017153 sodium:dicarboxylate symporter activity IBA --
genes like me logo Genes that share ontologies with SLC13A5: view
genes like me logo Genes that share phenotypes with SLC13A5: view

Human Phenotype Ontology for SLC13A5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC13A5 Gene

MGI Knock Outs for SLC13A5:

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for SLC13A5 Gene

Localization for SLC13A5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC13A5 Gene

Membrane; Multi-pass membrane protein. Cell membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC13A5 gene
Compartment Confidence
plasma membrane 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SLC13A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SLC13A5: view

Pathways & Interactions for SLC13A5 Gene

genes like me logo Genes that share pathways with SLC13A5: view

Interacting Proteins for SLC13A5 Gene

Gene Ontology (GO) - Biological Process for SLC13A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport IEA --
GO:0006842 tricarboxylic acid transport IEA --
GO:0015744 succinate transport IEA --
genes like me logo Genes that share ontologies with SLC13A5: view

No data available for SIGNOR curated interactions for SLC13A5 Gene

Drugs & Compounds for SLC13A5 Gene

(1) Drugs for SLC13A5 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Sodium Citrate Approved, Investigational Pharma Transporter, substrate 0

(1) Additional Compounds for SLC13A5 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Sodium
  • Sodium ion
7440-23-5
genes like me logo Genes that share compounds with SLC13A5: view

Transcripts for SLC13A5 Gene

Unigene Clusters for SLC13A5 Gene

Solute carrier family 13 (sodium-dependent citrate transporter), member 5:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC13A5 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - - - - -
SP2: - - - -
SP3: - -
SP4: - - - - -
SP5: -
SP6:
SP7: - - -
SP8:

Relevant External Links for SLC13A5 Gene

GeneLoc Exon Structure for
SLC13A5
ECgene alternative splicing isoforms for
SLC13A5

Expression for SLC13A5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC13A5 Gene

mRNA differential expression in normal tissues according to GTEx for SLC13A5 Gene

This gene is overexpressed in Liver (x47.4).

Protein differential expression in normal tissues from HIPED for SLC13A5 Gene

This gene is overexpressed in Liver (31.2), Fetal Liver (24.6), Frontal cortex (7.0), and Retina (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SLC13A5 Gene



Protein tissue co-expression partners for SLC13A5 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC13A5 Gene:

SLC13A5

SOURCE GeneReport for Unigene cluster for SLC13A5 Gene:

Hs.399496

mRNA Expression by UniProt/SwissProt for SLC13A5 Gene:

Q86YT5-S13A5_HUMAN
Tissue specificity: Expressed most predominantly in the liver, with moderate expression detectable in the brain and testis.

Evidence on tissue expression from TISSUES for SLC13A5 Gene

  • Liver(4.7)
  • Nervous system(4.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC13A5 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • face
  • forehead
  • head
  • lip
  • mouth
  • nose
  • pharynx
  • skull
Thorax:
  • chest wall
  • diaphragm
  • esophagus
  • lung
  • rib
  • rib cage
Abdomen:
  • abdominal wall
  • intestine
  • large intestine
  • stomach
Pelvis:
  • pelvis
  • rectum
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with SLC13A5: view

Orthologs for SLC13A5 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SLC13A5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC13A5 33 34
  • 99.18 (n)
cow
(Bos Taurus)
Mammalia SLC13A5 33 34
  • 87.31 (n)
dog
(Canis familiaris)
Mammalia SLC13A5 33 34
  • 85.92 (n)
rat
(Rattus norvegicus)
Mammalia Slc13a5 33
  • 81.46 (n)
mouse
(Mus musculus)
Mammalia Slc13a5 33 16 34
  • 80.11 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SLC13A5 34
  • 69 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SLC13A5 34
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLC13A5 33 34
  • 65.04 (n)
lizard
(Anolis carolinensis)
Reptilia SLC13A5 34
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slc13a5 33
  • 65.13 (n)
zebrafish
(Danio rerio)
Actinopterygii slc13a5a 33 34
  • 65.25 (n)
slc13a5b 34
  • 56 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Indy 34
  • 34 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea nac-3 34
  • 39 (a)
ManyToMany
nac-1 34
  • 38 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PHO91 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 37 (a)
ManyToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7160 33
Species where no ortholog for SLC13A5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC13A5 Gene

ENSEMBL:
Gene Tree for SLC13A5 (if available)
TreeFam:
Gene Tree for SLC13A5 (if available)

Paralogs for SLC13A5 Gene

Paralogs for SLC13A5 Gene

genes like me logo Genes that share paralogs with SLC13A5: view

Variants for SLC13A5 Gene

Sequence variations from dbSNP and Humsavar for SLC13A5 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1057519449 pathogenic, Epileptic encephalopathy, early infantile, 25 6,687,629(-) A/G 3_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant
rs138537951 likely-benign, not specified, Epileptic encephalopathy, early infantile, 25 6,707,115(-) G/A coding_sequence_variant, intron_variant, synonymous_variant
rs138834680 likely-benign, uncertain-significance, not specified, Epileptic encephalopathy, early infantile, 25 6,707,022(-) G/T intron_variant
rs138841868 uncertain-significance, Epileptic encephalopathy, early infantile, 25 6,695,837(-) G/A/T coding_sequence_variant, missense_variant
rs140940366 likely-benign, Epileptic encephalopathy, early infantile, 25 6,694,188(-) G/A coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC13A5 Gene

Variant ID Type Subtype PubMed ID
nsv574278 CNV gain 21841781

Variation tolerance for SLC13A5 Gene

Residual Variation Intolerance Score: 6.98% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.15; 23.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC13A5 Gene

Human Gene Mutation Database (HGMD)
SLC13A5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC13A5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC13A5 Gene

Disorders for SLC13A5 Gene

MalaCards: The human disease database

(6) MalaCards diseases for SLC13A5 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

S13A5_HUMAN
  • Epileptic encephalopathy, early infantile, 25 (EIEE25) [MIM:615905]: A disease characterized by seizures appearing in the first days of life, subclinical epileptic status, and recognizable EEG patterns with bilateral, multifocal status epilepticus. Patients have profound or severe delayed development with lack of speech, and most patients do not acquire the ability to sit. Additional variable features include axial hypotonia, peripheral hypertonia, and abnormal involuntary movements such as dystonia and choreoathetosis. {ECO:0000269 PubMed:24995870, ECO:0000269 PubMed:26384929}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SLC13A5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SLC13A5: view

No data available for Genatlas for SLC13A5 Gene

Publications for SLC13A5 Gene

  1. Human Na+ -coupled citrate transporter: primary structure, genomic organization, and transport function. (PMID: 12445824) Inoue K … Ganapathy V (Biochemical and biophysical research communications 2002) 2 3 4 22 58
  2. Recessive mutations in SLC13A5 result in a loss of citrate transport and cause neonatal epilepsy, developmental delay and teeth hypoplasia. (PMID: 26384929) Hardies K … autosomal recessive working group of the EuroEPINOMICS RES Consortium (Brain : a journal of neurology 2015) 3 4 58
  3. Mutations in SLC13A5 cause autosomal-recessive epileptic encephalopathy with seizure onset in the first days of life. (PMID: 24995870) Thevenon J … Rivière JB (American journal of human genetics 2014) 3 4 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. Identification of transport pathways for citric acid cycle intermediates in the human colon carcinoma cell line, Caco-2. (PMID: 18194662) Weerachayaphorn J … Pajor AM (Biochimica et biophysica acta 2008) 3 22 58

Products for SLC13A5 Gene

Sources for SLC13A5 Gene

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