Human Gene SLC44A1 (ENST00000374720.8_5) from GENCODE V47lift37
  Description: solute carrier family 44 member 1, transcript variant 1 (from RefSeq NM_080546.5)
Gencode Transcript: ENST00000374720.8_5
Gencode Gene: ENSG00000070214.17_9
Transcript (Including UTRs)
   Position: hg19 chr9:108,006,932-108,159,627 Size: 152,696 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr9:108,007,150-108,151,337 Size: 144,188 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:108,006,932-108,159,627)mRNA (may differ from genome)Protein (657 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CTL1_HUMAN
DESCRIPTION: RecName: Full=Choline transporter-like protein 1; AltName: Full=CDw92; AltName: Full=Solute carrier family 44 member 1; AltName: CD_antigen=CD92;
FUNCTION: Choline transporter. May be involved in membrane synthesis and myelin production.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein. Mitochondrion outer membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed in various cells of the hematopoietic system.
SIMILARITY: Belongs to the CTL (choline transporter-like) family.

-  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: SLC44A1
Diseases sorted by gene-association score: postural orthostatic tachycardia syndrome (18), choline deficiency disease (13), toxocariasis (10)

-  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: 42.89 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 423.42 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 -117.10218-0.537 Picture PostScript Text
3' UTR -2170.528290-0.262 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 Q8WWI5
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0015220 choline transmembrane transporter activity

Biological Process:
GO:0006656 phosphatidylcholine biosynthetic process
GO:0015871 choline transport
GO:0042426 choline catabolic process
GO:0055085 transmembrane transport

Cellular Component:
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF206464 - JP 2014500723-A/13967: Polycomb-Associated Non-Coding RNAs.
AJ272365 - Homo sapiens mRNA for human CD92 protein.
AJ420812 - Homo sapiens mRNA for choline transporter-like protein 1, splice variant a (CTL1 gene).
BC049203 - Homo sapiens solute carrier family 44, member 1, mRNA (cDNA clone MGC:51770 IMAGE:5492167), complete cds.
AB528737 - Synthetic construct DNA, clone: pF1KB9940, Homo sapiens SLC44A1 gene for solute carrier family 44, member 1, without stop codon, in Flexi system.
AK022549 - Homo sapiens cDNA FLJ12487 fis, clone NT2RM2000609, highly similar to Choline transporter-like protein 1.
AK124926 - Homo sapiens cDNA FLJ42936 fis, clone BRSSN2014424, highly similar to Choline transporter-like protein 1.
BC018213 - Homo sapiens solute carrier family 44, member 1, mRNA (cDNA clone IMAGE:3882479), partial cds.
MA442041 - JP 2018138019-A/13967: Polycomb-Associated Non-Coding RNAs.
LF354735 - JP 2014500723-A/162238: Polycomb-Associated Non-Coding RNAs.
LF354740 - JP 2014500723-A/162243: Polycomb-Associated Non-Coding RNAs.
MA590312 - JP 2018138019-A/162238: Polycomb-Associated Non-Coding RNAs.
MA590317 - JP 2018138019-A/162243: Polycomb-Associated Non-Coding RNAs.
JD205404 - Sequence 186428 from Patent EP1572962.
LF354742 - JP 2014500723-A/162245: Polycomb-Associated Non-Coding RNAs.
LF354743 - JP 2014500723-A/162246: Polycomb-Associated Non-Coding RNAs.
JD553842 - Sequence 534866 from Patent EP1572962.
JD486231 - Sequence 467255 from Patent EP1572962.
JD536294 - Sequence 517318 from Patent EP1572962.
JD121160 - Sequence 102184 from Patent EP1572962.
LF354744 - JP 2014500723-A/162247: Polycomb-Associated Non-Coding RNAs.
JD316300 - Sequence 297324 from Patent EP1572962.
JD369333 - Sequence 350357 from Patent EP1572962.
JD088677 - Sequence 69701 from Patent EP1572962.
JD036601 - Sequence 17625 from Patent EP1572962.
LF354745 - JP 2014500723-A/162248: Polycomb-Associated Non-Coding RNAs.
JD188332 - Sequence 169356 from Patent EP1572962.
LF354746 - JP 2014500723-A/162249: Polycomb-Associated Non-Coding RNAs.
AK000109 - Homo sapiens cDNA FLJ20102 fis, clone COL04783.
LF354747 - JP 2014500723-A/162250: Polycomb-Associated Non-Coding RNAs.
LF354748 - JP 2014500723-A/162251: Polycomb-Associated Non-Coding RNAs.
LF354749 - JP 2014500723-A/162252: Polycomb-Associated Non-Coding RNAs.
JD378549 - Sequence 359573 from Patent EP1572962.
JD234408 - Sequence 215432 from Patent EP1572962.
JD428064 - Sequence 409088 from Patent EP1572962.
JD511179 - Sequence 492203 from Patent EP1572962.
JD371184 - Sequence 352208 from Patent EP1572962.
JD227327 - Sequence 208351 from Patent EP1572962.
LF354750 - JP 2014500723-A/162253: Polycomb-Associated Non-Coding RNAs.
MA590319 - JP 2018138019-A/162245: Polycomb-Associated Non-Coding RNAs.
MA590320 - JP 2018138019-A/162246: Polycomb-Associated Non-Coding RNAs.
MA590321 - JP 2018138019-A/162247: Polycomb-Associated Non-Coding RNAs.
MA590322 - JP 2018138019-A/162248: Polycomb-Associated Non-Coding RNAs.
MA590323 - JP 2018138019-A/162249: Polycomb-Associated Non-Coding RNAs.
MA590324 - JP 2018138019-A/162250: Polycomb-Associated Non-Coding RNAs.
MA590325 - JP 2018138019-A/162251: Polycomb-Associated Non-Coding RNAs.
MA590326 - JP 2018138019-A/162252: Polycomb-Associated Non-Coding RNAs.
MA590327 - JP 2018138019-A/162253: Polycomb-Associated Non-Coding RNAs.

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

Protein Q8WWI5 (Reactome details) participates in the following event(s):

R-HSA-6797956 SLC44A1 transports Cho from cytosol to mitochondrial matrix
R-HSA-444433 Cho transports from the extracellular space to the cytosol
R-HSA-6798163 Choline catabolism
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-71291 Metabolism of nitrogenous molecules
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-1430728 Metabolism
R-HSA-382551 Transport of small molecules
R-HSA-1483257 Phospholipid metabolism
R-HSA-556833 Metabolism of lipids

-  Other Names for This Gene
  Alternate Gene Symbols: A6NLZ9, CD92, CDW92, CTL1, CTL1_HUMAN, ENST00000374720.1, ENST00000374720.2, ENST00000374720.3, ENST00000374720.4, ENST00000374720.5, ENST00000374720.6, ENST00000374720.7, NM_080546, Q5VUB3, Q8WVB0, Q8WWI5, Q96KU3, Q9NY69, SLC44A1 , uc318ltw.1, uc318ltw.2
UCSC ID: ENST00000374720.8_5
RefSeq Accession: NM_080546.5
Protein: Q8WWI5 (aka CTL1_HUMAN)

-  Gene Model Information
  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.