Human Gene SLC25A1 (uc021wlb.2) Description and Page Index
  Description: Homo sapiens solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 (SLC25A1), transcript variant 3, mRNA.
RefSeq Summary (NM_001256534): This gene encodes a member of the mitochondrial carrier subfamily of solute carrier proteins. Members of this family include nuclear-encoded transporters that translocate small metabolites across the mitochondrial membrane. This protein regulates the movement of citrate across the inner membranes of the mitochondria. Mutations in this gene have been associated with combined D-2- and L-2-hydroxyglutaric aciduria. Pseudogenes of this gene have been identified on chromosomes 7, 11, 16, and 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013].
Transcript (Including UTRs)
   Position: hg19 chr22:19,163,088-19,166,018 Size: 2,931 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr22:19,163,643-19,165,868 Size: 2,226 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:19,163,088-19,166,018)mRNA (may differ from genome)Protein (318 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIOMIMPubMed
Stanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: D9HTE9_HUMAN
DESCRIPTION: SubName: Full=Plasma membrane citrate carrier;
SIMILARITY: Belongs to the mitochondrial carrier family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLC25A1
CDC HuGE Published Literature: SLC25A1

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC25A1
Diseases sorted by gene-association score: combined d-2- and l-2-hydroxyglutaric aciduria* (1705), presynaptic congenital myasthenic syndromes* (157), l-2-hydroxyglutaric aciduria (42), 2-hydroxyglutaric aciduria (34), velocardiofacial syndrome (6), optic nerve hypoplasia (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 60.94 RPKM in Liver
Total median expression: 1418.68 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 -84.00150-0.560 Picture PostScript Text
3' UTR -218.04555-0.393 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
IPR018108 - Mitochondrial_sb/sol_carrier
IPR023395 - Mt_carrier_dom

Pfam Domains:
PF00153 - Mitochondrial carrier protein

SCOP Domains:
103506 - Mitochondrial carrier

ModBase Predicted Comparative 3D Structure on D9HTE9
FrontTopSide
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  DQ892916 - Synthetic construct clone IMAGE:100005546; FLH190800.01X; RZPDo839E0276D solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 (SLC25A1) gene, encodes complete protein.
DQ896165 - Synthetic construct Homo sapiens clone IMAGE:100010625; FLH190796.01L; RZPDo839E0266D solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 (SLC25A1) gene, encodes complete protein.
DQ896170 - Synthetic construct Homo sapiens clone IMAGE:100010630; FLH263624.01L; RZPDo839E1066D solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 (SLC25A1) gene, encodes complete protein.
LF210535 - JP 2014500723-A/18038: Polycomb-Associated Non-Coding RNAs.
L77567 - Homo sapiens mitochondrial citrate transport protein (CTP) mRNA, 3' end.
HM037273 - Homo sapiens plasma membrane citrate carrier (SLC25A1) mRNA, complete cds.
BC018590 - Homo sapiens solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1, mRNA (cDNA clone IMAGE:3868835).
BC004980 - Homo sapiens solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1, mRNA (cDNA clone MGC:3876 IMAGE:2957917), complete cds.
BC008061 - Homo sapiens solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1, mRNA (cDNA clone MGC:2151 IMAGE:2958945), complete cds.
AX229889 - Sequence 15 from Patent WO0162959.
L75823 - Homo sapiens citrate transport protein mRNA, complete cds; nuclear gene for mitochondrial product.
JD514780 - Sequence 495804 from Patent EP1572962.
JD121514 - Sequence 102538 from Patent EP1572962.
U25147 - Human citrate transporter protein mRNA, nuclear gene encoding mitochondrial protein, complete cds.
JD399373 - Sequence 380397 from Patent EP1572962.
JD195215 - Sequence 176239 from Patent EP1572962.
JD393005 - Sequence 374029 from Patent EP1572962.
JD287350 - Sequence 268374 from Patent EP1572962.
JD163300 - Sequence 144324 from Patent EP1572962.
JD409618 - Sequence 390642 from Patent EP1572962.
AK292313 - Homo sapiens cDNA FLJ75289 complete cds, highly similar to Homo sapiens solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 (SLC25A1), mRNA.
JD058245 - Sequence 39269 from Patent EP1572962.
JD531282 - Sequence 512306 from Patent EP1572962.
JD495251 - Sequence 476275 from Patent EP1572962.
JD528037 - Sequence 509061 from Patent EP1572962.
JD444326 - Sequence 425350 from Patent EP1572962.
AK298204 - Homo sapiens cDNA FLJ60026 complete cds, highly similar to Tricarboxylate transport protein, mitochondrial precursor.
JD405682 - Sequence 386706 from Patent EP1572962.
KJ897578 - Synthetic construct Homo sapiens clone ccsbBroadEn_06972 SLC25A1 gene, encodes complete protein.
LF338603 - JP 2014500723-A/146106: Polycomb-Associated Non-Coding RNAs.
LF338604 - JP 2014500723-A/146107: Polycomb-Associated Non-Coding RNAs.
LF338605 - JP 2014500723-A/146108: Polycomb-Associated Non-Coding RNAs.
LF338606 - JP 2014500723-A/146109: Polycomb-Associated Non-Coding RNAs.
JD249056 - Sequence 230080 from Patent EP1572962.
JD022910 - Sequence 3934 from Patent EP1572962.
JD027770 - Sequence 8794 from Patent EP1572962.
LF338607 - JP 2014500723-A/146110: Polycomb-Associated Non-Coding RNAs.
MA446112 - JP 2018138019-A/18038: Polycomb-Associated Non-Coding RNAs.
MA574180 - JP 2018138019-A/146106: Polycomb-Associated Non-Coding RNAs.
MA574181 - JP 2018138019-A/146107: Polycomb-Associated Non-Coding RNAs.
MA574182 - JP 2018138019-A/146108: Polycomb-Associated Non-Coding RNAs.
MA574183 - JP 2018138019-A/146109: Polycomb-Associated Non-Coding RNAs.
MA574184 - JP 2018138019-A/146110: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_malatexPathway - Shuttle for transfer of acetyl groups from mitochondria to the cytosol

-  Other Names for This Gene
  Alternate Gene Symbols: D9HTE9, D9HTE9_HUMAN, NM_001256534, NP_001243463, uc021wlb.1
UCSC ID: uc021wlb.2
RefSeq Accession: NM_001256534
Protein: D9HTE9

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SLC25A1:
cms (Congenital Myasthenic Syndromes)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001256534.1
exon count: 8CDS single in 3' UTR: no RNA size: 1680
ORF size: 957CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1990.00frame shift in genome: no % Coverage: 98.93
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 265# strange splices: 0
Click here for a detailed description of the fields of the table above.

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