Human Gene SLC25A13 (ENST00000265631.10) from GENCODE V44
  Description: Homo sapiens solute carrier family 25 member 13 (SLC25A13), transcript variant 3, non-coding RNA. (from RefSeq NR_027662)
RefSeq Summary (NM_014251): This gene is a member of the mitochondrial carrier family. The encoded protein contains four EF-hand Ca(2+) binding motifs in the N-terminal domain, and localizes to mitochondria. The protein catalyzes the exchange of aspartate for glutamate and a proton across the inner mitochondrial membrane, and is stimulated by calcium on the external side of the inner mitochondrial membrane. Mutations in this gene result in citrullinemia, type II. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009].
Gencode Transcript: ENST00000265631.10
Gencode Gene: ENSG00000004864.14
Transcript (Including UTRs)
   Position: hg38 chr7:96,120,220-96,322,098 Size: 201,879 Total Exon Count: 18 Strand: -
Coding Region
   Position: hg38 chr7:96,121,191-96,321,956 Size: 200,766 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:96,120,220-96,322,098)mRNA (may differ from genome)Protein (675 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CMC2_HUMAN
DESCRIPTION: RecName: Full=Calcium-binding mitochondrial carrier protein Aralar2; AltName: Full=Citrin; AltName: Full=Mitochondrial aspartate glutamate carrier 2; AltName: Full=Solute carrier family 25 member 13;
FUNCTION: Catalyzes the calcium-dependent exchange of cytoplasmic glutamate with mitochondrial aspartate across the mitochondrial inner membrane. May have a function in the urea cycle.
SUBCELLULAR LOCATION: Mitochondrion inner membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: High levels in liver and low levels in kidney, pancreas, placenta, heart and brain.
DISEASE: Defects in SLC25A13 are the cause of citrullinemia type 2 (CTLN2) [MIM:603471]. Citrullinemia belongs to the urea cycle disorders. It is an autosomal recessive disease characterized primarily by elevated serum and urine citrulline levels. Ammonia intoxication is another manifestation. CTLN2 is characterized by neuropsychiatric symptoms including abnormal behaviors, loss of memory, seizures and coma. Death can result from brain edema. Onset is sudden and usually between the ages of 20 and 50 years.
DISEASE: Defects in SLC25A13 are the cause of neonatal intrahepatic cholestasis due to citrin deficiency (NICCD) [MIM:605814]. NICCD is a form of citrullinemia type 2 with neonatal onset. NICCD is characterized by suppression of the bile flow, hepatic fibrosis, low birth weight, growth retardation, hypoproteinemia, variable liver dysfunction. NICCD is generally not severe and symptoms disappear by one year of age with an appropriate diet. Years or even decades later, however, some individuals develop the characteristic features of citrullinemia type 2 with neuropsychiatric symptoms.
MISCELLANEOUS: Binds calcium.
SIMILARITY: Belongs to the mitochondrial carrier family.
SIMILARITY: Contains 4 EF-hand domains.
SIMILARITY: Contains 3 Solcar repeats.
SEQUENCE CAUTION: Sequence=AAB67049.1; Type=Erroneous gene model prediction; Sequence=AAB70112.1; Type=Erroneous gene model prediction;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SLC25A13";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SLC25A13
Diseases sorted by gene-association score: citrullinemia, type ii, neonatal-onset* (1550), citrullinemia, adult-onset type ii* (1472), citrullinemia (43), cholestasis (27), intrahepatic cholestasis (22), failure to thrive and dyslipidemia caused by citrin deficiency (19), brain edema (17), hepatic encephalopathy (15), obstructive jaundice (15), galactosemia (12), galactokinase deficiency with cataracts (9), duodenal somatostatinoma (9), urea cycle disorder (8), bile duct disease (7), vlcad deficiency (7), ovarian cyst (7), acyl-coa dehydrogenase, short-chain, deficiency of (7), fatty acid oxidation disorders (6), autosomal recessive disease (6), biliary tract disease (6), holocarboxylase synthetase deficiency (6), liver disease (5), propionicacidemia (4)
* = Manually curated disease association

-  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: 28.32 RPKM in Liver
Total median expression: 310.59 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.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -49.90142-0.351 Picture PostScript Text
3' UTR -238.00971-0.245 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011992 - EF-hand-like_dom
IPR018249 - EF_HAND_2
IPR002048 - EF_hand_Ca-bd
IPR002067 - Mit_carrier
IPR018108 - Mitochondrial_sb/sol_carrier
IPR023395 - Mt_carrier_dom

Pfam Domains:
PF00153 - Mitochondrial carrier protein

ModBase Predicted Comparative 3D Structure on Q9UJS0
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
Genome BrowserNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
MGI    SGD
Protein Sequence    Protein Sequence
Alignment    Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005215 transporter activity
GO:0005313 L-glutamate transmembrane transporter activity
GO:0005509 calcium ion binding
GO:0015172 acidic amino acid transmembrane transporter activity
GO:0015183 L-aspartate transmembrane transporter activity
GO:0046872 metal ion binding

Biological Process:
GO:0006094 gluconeogenesis
GO:0006754 ATP biosynthetic process
GO:0006839 mitochondrial transport
GO:0015810 aspartate transport
GO:0015813 L-glutamate transport
GO:0043490 malate-aspartate shuttle
GO:0045333 cellular respiration
GO:0051592 response to calcium ion
GO:0055085 transmembrane transport
GO:0070778 L-aspartate transport

Cellular Component:
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC006566 - Homo sapiens solute carrier family 25, member 13 (citrin), mRNA (cDNA clone MGC:3379 IMAGE:3604257), complete cds.
AJ496569 - Homo sapiens mRNA for mitochondrial aspartate-glutamate carrier protein (SLC25A13 gene).
AF118838 - Homo sapiens citrin (SLC25A13) mRNA, complete cds.
AK025779 - Homo sapiens cDNA: FLJ22126 fis, clone HEP19479, highly similar to AF118838 Homo sapiens citrin (SLC25A13) mRNA.
AK000766 - Homo sapiens cDNA FLJ20759 fis, clone HEP01251, highly similar to AF118838 Homo sapiens citrin.
AK222864 - Homo sapiens mRNA for solute carrier family 25, member 13 (citrin) variant, clone: HEP14393.
AK025227 - Homo sapiens cDNA: FLJ21574 fis, clone COL06668, highly similar to AF118838 Homo sapiens citrin (SLC25A13) mRNA.
AK294629 - Homo sapiens cDNA FLJ54671 complete cds, highly similar to Calcium-binding mitochondrial carrier protein Aralar2.
Y17571 - Homo sapiens mRNA for mitochondrial carrier protein ARALAR2.
DQ892851 - Synthetic construct clone IMAGE:100005481; FLH190297.01X; RZPDo839G0975D solute carrier family 25, member 13 (citrin) (SLC25A13) gene, encodes complete protein.
DQ896098 - Synthetic construct Homo sapiens clone IMAGE:100010558; FLH190293.01L; RZPDo839G0965D solute carrier family 25, member 13 (citrin) (SLC25A13) gene, encodes complete protein.
KJ892943 - Synthetic construct Homo sapiens clone ccsbBroadEn_02337 SLC25A13 gene, encodes complete protein.
KR710271 - Synthetic construct Homo sapiens clone CCSBHm_00011021 SLC25A13 (SLC25A13) mRNA, encodes complete protein.
KR710272 - Synthetic construct Homo sapiens clone CCSBHm_00011030 SLC25A13 (SLC25A13) mRNA, encodes complete protein.
KR710273 - Synthetic construct Homo sapiens clone CCSBHm_00011031 SLC25A13 (SLC25A13) mRNA, encodes complete protein.
KR710274 - Synthetic construct Homo sapiens clone CCSBHm_00011038 SLC25A13 (SLC25A13) mRNA, encodes complete protein.
CU675453 - Synthetic construct Homo sapiens gateway clone IMAGE:100018408 5' read SLC25A13 mRNA.
JD503825 - Sequence 484849 from Patent EP1572962.
JD244751 - Sequence 225775 from Patent EP1572962.
JD270987 - Sequence 252011 from Patent EP1572962.
JD290134 - Sequence 271158 from Patent EP1572962.
JD188162 - Sequence 169186 from Patent EP1572962.
JD037420 - Sequence 18444 from Patent EP1572962.
JD214314 - Sequence 195338 from Patent EP1572962.
JD349836 - Sequence 330860 from Patent EP1572962.
JD257845 - Sequence 238869 from Patent EP1572962.
JD222300 - Sequence 203324 from Patent EP1572962.
JD307794 - Sequence 288818 from Patent EP1572962.
JD377794 - Sequence 358818 from Patent EP1572962.
JD156435 - Sequence 137459 from Patent EP1572962.
AK130552 - Homo sapiens cDNA FLJ27042 fis, clone SLV08949.
JD124650 - Sequence 105674 from Patent EP1572962.
JD405886 - Sequence 386910 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UJS0 (Reactome details) participates in the following event(s):

R-HSA-1299484 TIMM8:TIMM13 chaperones hydrophobic proteins
R-HSA-372448 SLC25A12,13 exchange cytosolic L-Glu for mitochondrial matrix L-Asp
R-HSA-1268020 Mitochondrial protein import
R-HSA-70263 Gluconeogenesis
R-HSA-392499 Metabolism of proteins
R-HSA-70326 Glucose metabolism
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: ARALAR2, CMC2_HUMAN, ENST00000265631.1, ENST00000265631.2, ENST00000265631.3, ENST00000265631.4, ENST00000265631.5, ENST00000265631.6, ENST00000265631.7, ENST00000265631.8, ENST00000265631.9, NR_027662, O14566, O14575, Q546F9, Q9NZW1, Q9UJS0, Q9UNI7, uc003uof.1, uc003uof.2, uc003uof.3, uc003uof.4, uc003uof.5, uc003uof.6
UCSC ID: ENST00000265631.10
RefSeq Accession: NM_014251
Protein: Q9UJS0 (aka CMC2_HUMAN)
CCDS: CCDS5645.1, CCDS55130.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SLC25A13:
citrin (Citrin Deficiency)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.