Human Gene SLC44A3 (ENST00000271227.11_7) from GENCODE V47lift37

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Description: solute carrier family 44 member 3, transcript variant 9 (from RefSeq NR_146575.2)
Gencode Transcript: ENST00000271227.11_7
Gencode Gene: ENSG00000143036.17_13
Transcript (Including UTRs)
Position: hg19 chr1:95,285,913-95,360,802 Size: 74,890 Total Exon Count: 15 Strand: +
Coding Region
Position: hg19 chr1:95,286,008-95,360,478 Size: 74,471 Coding Exon Count: 15

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr1:95,285,913-95,360,802)			mRNA (may differ from genome)		Protein (653 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	MGI	PubMed	Reactome	UniProtKB	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: CTL3_HUMAN DESCRIPTION: RecName: Full=Choline transporter-like protein 3; AltName: Full=Solute carrier family 44 member 3; SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (By similarity). SIMILARITY: Belongs to the CTL (choline transporter-like) family. SEQUENCE CAUTION: Sequence=AAH33858.2; Type=Erroneous initiation; Sequence=AAQ89022.1; Type=Erroneous initiation;

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

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene C547126 AZM551248 D001564 Benzo(a)pyrene D002794 Choline D019327 Copper Sulfate D016572 Cyclosporine D004051 Diethylhexyl Phthalate D005492 Folic Acid D008715 Methionine C558013 NSC 689534 D011374 Progesterone more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 13.73 RPKM in Colon - Transverse Total median expression: 161.25 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-49.10	95	-0.517	Picture	PostScript	Text
3' UTR	-58.80	324	-0.181	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
IPR007603 - Choline_transptr-like

Pfam Domains:
PF04515 - Plasma-membrane choline transporter

ModBase Predicted Comparative 3D Structure on Q8N4M1


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0005515 protein binding GO:0015220 choline transmembrane transporter activity Biological Process: GO:0006656 phosphatidylcholine biosynthetic process GO:0015871 choline transport GO:0055085 transmembrane transport Cellular Component: GO:0005886 plasma membrane GO:0016020 membrane GO:0016021 integral component of membrane

Descriptions from all associated GenBank mRNAs


	AK303906 - Homo sapiens cDNA FLJ56200 complete cds, highly similar to Choline transporter-like protein 3. BC033858 - Homo sapiens solute carrier family 44, member 3, mRNA (cDNA clone IMAGE:5174513), partial cds. AX721168 - Sequence 128 from Patent WO0220754. AK301288 - Homo sapiens cDNA FLJ54390 complete cds, highly similar to Choline transporter-like protein 3. AK316123 - Homo sapiens cDNA, FLJ79022 complete cds, highly similar to Choline transporter-like protein 3. AK313574 - Homo sapiens cDNA, FLJ94138. BC053877 - Homo sapiens solute carrier family 44, member 3, mRNA (cDNA clone MGC:61744 IMAGE:5760394), complete cds. AK300193 - Homo sapiens cDNA FLJ50210 complete cds, highly similar to Choline transporter-like protein 3. LF206322 - JP 2014500723-A/13825: Polycomb-Associated Non-Coding RNAs. JD343369 - Sequence 324393 from Patent EP1572962. MA441899 - JP 2018138019-A/13825: Polycomb-Associated Non-Coding RNAs. BX648225 - Homo sapiens mRNA; cDNA DKFZp779E1542 (from clone DKFZp779E1542). HQ257925 - Synthetic construct Homo sapiens clone IMAGE:100072234 solute carrier family 44, member 3 (SLC44A3), transcript variant 2 (SLC44A3) gene, encodes complete protein. KJ900111 - Synthetic construct Homo sapiens clone ccsbBroadEn_09505 SLC44A3 gene, encodes complete protein. AK302381 - Homo sapiens cDNA FLJ50295 complete cds, highly similar to Choline transporter-like protein 3. AY358659 - Homo sapiens clone DNA56868 SGRD558 (UNQ558) mRNA, complete cds. BC040448 - Homo sapiens solute carrier family 44, member 3, mRNA (cDNA clone IMAGE:5763274). JD456334 - Sequence 437358 from Patent EP1572962. JD061472 - Sequence 42496 from Patent EP1572962.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q8N4M1 (Reactome details) participates in the following event(s): R-HSA-444433 Cho transports from the extracellular space to the cytosol R-HSA-425366 Transport of bile salts and organic acids, metal ions and amine compounds R-HSA-425428 Amine compound SLC transporters R-HSA-1483191 Synthesis of PC R-HSA-425407 SLC-mediated transmembrane transport R-HSA-1483206 Glycerophospholipid biosynthesis R-HSA-382551 Transport of small molecules R-HSA-1483257 Phospholipid metabolism R-HSA-556833 Metabolism of lipids R-HSA-1430728 Metabolism

Other Names for This Gene


	Alternate Gene Symbols: B4DVY4, B4E1M4, B7ZA08, CTL3, CTL3_HUMAN, E9PJH2, E9PJY8, ENST00000271227.1, ENST00000271227.10, ENST00000271227.2, ENST00000271227.3, ENST00000271227.4, ENST00000271227.5, ENST00000271227.6, ENST00000271227.7, ENST00000271227.8, ENST00000271227.9, NR_146575, Q6UWT1, Q7Z6C5, Q8N4M1, Q9BWY7, uc317ivp.1, uc317ivp.2, UNQ558/PRO1115 UCSC ID: ENST00000271227.11_7 RefSeq Accession: NM_001114106.3 Protein: Q8N4M1 (aka CTL3_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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