Slc13a5 solute carrier family 13 (sodium-dependent citrate transporter), member 5 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Slc13a5provided by MGI
Official Full Name: solute carrier family 13 (sodium-dependent citrate transporter), member 5provided by MGI
Primary source: MGI:MGI:3037150
See related: Ensembl:ENSMUSG00000020805 AllianceGenome:MGI:3037150
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Indy; Nact; mINDY; NaC2/NaCT
Summary: Enables citrate transmembrane transporter activity; organic acid:sodium symporter activity; and succinate transmembrane transporter activity. Involved in carboxylic acid transport and cellular response to lithium ion. Acts upstream of or within succinate transport and tricarboxylic acid transport. Predicted to be located in basolateral plasma membrane; cytosol; and nucleoplasm. Predicted to be integral component of membrane. Is expressed in forelimb and humerus cartilage condensation. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 25. Orthologous to human SLC13A5 (solute carrier family 13 member 5). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in testis adult (RPKM 17.5), cortex adult (RPKM 3.2) and 4 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 B4; 11 43.95 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (72132816..72158092, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (72241990..72267295, complement)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Disruption of the sodium-dependent citrate transporter SLC13A5 in mice causes alterations in brain citrate levels and neuronal network excitability in the hippocampus.
Title: Disruption of the sodium-dependent citrate transporter SLC13A5 in mice causes alterations in brain citrate levels and neuronal network excitability in the hippocampus.
Nervous System Deletion of Mammalian INDY in Mice Mimics Dietary Restriction-Induced Memory Enhancement.
Title: Nervous System Deletion of Mammalian INDY in Mice Mimics Dietary Restriction-Induced Memory Enhancement.
Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
Title: Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
The longevity gene mIndy (I'm Not Dead, Yet) affects blood pressure through sympathoadrenal mechanisms.
Title: The longevity gene mIndy (I'm Not Dead, Yet) affects blood pressure through sympathoadrenal mechanisms.
The findings revealed the potentially important role of citrate and Slc13a5 in the development and function of teeth and bone.
Title: Defective enamel and bone development in sodium-dependent citrate transporter (NaCT) Slc13a5 deficient mice.
Our studies demonstrate a profound effect of mIndy on mammalian energy metabolism.
Title: Deletion of the mammalian INDY homolog mimics aspects of dietary restriction and protects against adiposity and insulin resistance in mice.
Molecular cloning and transport properties of NaCT.
Title: Functional features and genomic organization of mouse NaCT, a sodium-coupled transporter for tricarboxylic acid cycle intermediates.
Na+ -coupled di/tricarboxylate transport system expressed in neurons as NaC2/NaCT, which can transport the tricarboxylate citrate as well as dicarboxylates such as succinate, alpha-ketoglutarate, and malate.
Title: Functional characterization of Na+ -coupled citrate transporter NaC2/NaCT expressed in primary cultures of neurons from mouse cerebral cortex.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (7) 1 citation
Chemically induced (ENU) (2)
Endonuclease-mediated (5)

General gene information

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Markers

Slc13a5 (e-PCR), detects polymorphism
- UniSTS:498447

Slc13a5 (e-PCR), detects polymorphism
- UniSTS:498355

Slc13a5 (e-PCR), detects polymorphism
- UniSTS:546996

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables citrate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables citrate transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables citrate transmembrane transporter activity	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables organic acid:sodium symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables organic acid:sodium symporter activity	ISO Inferred from Sequence Orthology more info
enables sodium:dicarboxylate symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables sodium:dicarboxylate symporter activity	ISO Inferred from Sequence Orthology more info
enables succinate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables succinate transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables succinate transmembrane transporter activity	ISO Inferred from Sequence Orthology more info
enables symporter activity	IEA Inferred from Electronic Annotation more info
enables transmembrane transporter activity	IEA Inferred from Electronic Annotation more info
enables tricarboxylic acid transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in alpha-ketoglutarate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in alpha-ketoglutarate transport	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lithium ion	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to lithium ion	ISO Inferred from Sequence Orthology more info
involved_in citrate transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within citrate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in citrate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in citrate transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in citrate transport	ISO Inferred from Sequence Orthology more info
involved_in fumarate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in fumarate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in fumarate transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within monoatomic ion transport	IEA Inferred from Electronic Annotation more info
involved_in oxaloacetate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in oxaloacetate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in oxaloacetate transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sodium ion transport	IEA Inferred from Electronic Annotation more info
involved_in succinate transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within succinate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in succinate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in succinate transport	ISO Inferred from Sequence Orthology more info
involved_in transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within tricarboxylic acid transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within tricarboxylic acid transport	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in basolateral plasma membrane	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: Na(+)/citrate cotransporter

Names: novel solute carrier family 13 (sodium-dependent dicarboxylate transporter) (Slc13a2 or 3) member; sodium-coupled citrate transporter; sodium-dependent citrate transporter; solute carrier family 13 member 5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001004148.5 → NP_001004148.1 Na(+)/citrate cotransporter isoform 1

See identical proteins and their annotated locations for NP_001004148.1

Status: VALIDATED

Source sequence(s)

AL929071

Consensus CDS

CCDS24983.1

UniProtKB/Swiss-Prot

Q67BT3

UniProtKB/TrEMBL

A0A140LIR1

Related

ENSMUSP00000021161.7, ENSMUST00000021161.14

Conserved Domains (1) summary

cl21473
Location:13 → 558

ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...
NM_001372402.1 → NP_001359331.1 Na(+)/citrate cotransporter isoform 2

Status: VALIDATED

Source sequence(s)

AL929071

UniProtKB/TrEMBL

A0A140LIR1

Conserved Domains (1) summary

cl21473
Location:50 → 595

ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...
NM_001372403.1 → NP_001359332.1 Na(+)/citrate cotransporter isoform 3

Status: VALIDATED

Source sequence(s)

AL929071

UniProtKB/TrEMBL

A0A140LIR1

Conserved Domains (1) summary

cd01115
Location:39 → 475

SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000077.7 Reference GRCm39 C57BL/6J

Range

72132816..72158092 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036156658.1 → XP_036012551.1 Na(+)/citrate cotransporter isoform X3

UniProtKB/TrEMBL

A0A140LIR1

Conserved Domains (1) summary

cd01115
Location:76 → 512

SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...
XM_017314526.3 → XP_017170015.1 Na(+)/citrate cotransporter isoform X1

UniProtKB/TrEMBL

A0A140LIR1

Conserved Domains (1) summary

cl21473
Location:50 → 566

ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...
XM_017314527.3 → XP_017170016.1 Na(+)/citrate cotransporter isoform X2

Conserved Domains (1) summary

cd01115
Location:76 → 493

SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...
XM_017314528.1 → XP_017170017.1 Na(+)/citrate cotransporter isoform X4

Conserved Domains (1) summary

cl21473
Location:2 → 405

ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...