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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for SLC44A1

check button Gene summary
Gene informationGene symbol

SLC44A1

Gene ID

23446

Gene namesolute carrier family 44 member 1
SynonymsCD92|CDW92|CHTL1|CTL1
Cytomap

9q31.1-q31.2

Type of geneprotein-coding
Descriptioncholine transporter-like protein 1CDW92 antigensolute carrier family 44 (choline transporter), member 1
Modification date20180519
UniProtAcc

Q8WWI5

ContextPubMed: SLC44A1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID

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Exon skipping events across known transcript of Ensembl for SLC44A1 from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Gene isoform structures and expression levels for SLC44A1

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for SLC44A1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4979129108061500:108061590:108062023:108062218:108072004:108072147108062023:108062218ENSG00000070214.11ENST00000607692.1
exon_skip_4979159108061500:108061590:108072004:108072147:108097843:108097868108072004:108072147ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374724.1,ENST00000374720.3
exon_skip_4979229108072029:108072147:108097843:108097980:108110638:108110732108097843:108097980ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374724.1,ENST00000374720.3
exon_skip_4979259108110638:108110732:108118492:108118662:108120624:108120714108118492:108118662ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374724.1,ENST00000374720.3
exon_skip_4979299108127763:108127920:108128626:108128710:108136878:108137016108128626:108128710ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374724.1,ENST00000374720.3,ENST00000343170.7
exon_skip_4979309108128626:108128710:108136878:108137016:108145403:108145640108136878:108137016ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374724.1,ENST00000374720.3,ENST00000343170.7
exon_skip_4979319108136878:108137016:108145403:108145640:108147702:108147783108145403:108145640ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374724.1,ENST00000374720.3,ENST00000343170.7
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENSG00000070214.11ENST00000470972.1,ENST00000374720.3
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENSG00000070214.11ENST00000374724.1,ENST00000343170.7

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for SLC44A1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4979129108061500:108061590:108062023:108062218:108072004:108072147108062023:108062218ENSG00000070214.11ENST00000607692.1
exon_skip_4979159108061500:108061590:108072004:108072147:108097843:108097868108072004:108072147ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374720.3,ENST00000374724.1
exon_skip_4979229108072029:108072147:108097843:108097980:108110638:108110732108097843:108097980ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374720.3,ENST00000374724.1
exon_skip_4979259108110638:108110732:108118492:108118662:108120624:108120714108118492:108118662ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374720.3,ENST00000374724.1
exon_skip_4979299108127763:108127920:108128626:108128710:108136878:108137016108128626:108128710ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374720.3,ENST00000374724.1,ENST00000343170.7
exon_skip_4979309108128626:108128710:108136878:108137016:108145403:108145640108136878:108137016ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374720.3,ENST00000374724.1,ENST00000343170.7
exon_skip_4979319108136878:108137016:108145403:108145640:108147702:108147783108145403:108145640ENSG00000070214.11ENST00000374723.1,ENST00000470972.1,ENST00000374720.3,ENST00000374724.1,ENST00000343170.7
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENSG00000070214.11ENST00000470972.1,ENST00000374720.3
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENSG00000070214.11ENST00000374724.1,ENST00000343170.7

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for SLC44A1

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000374720108072004108072147Frame-shift
ENST00000374720108097843108097980Frame-shift
ENST00000374720108118492108118662Frame-shift
ENST00000374720108128626108128710In-frame
ENST00000374720108136878108137016In-frame
ENST00000374720108145403108145640In-frame
ENST00000374720108147702108147783In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000374720108072004108072147Frame-shift
ENST00000374720108097843108097980Frame-shift
ENST00000374720108118492108118662Frame-shift
ENST00000374720108128626108128710In-frame
ENST00000374720108136878108137016In-frame
ENST00000374720108145403108145640In-frame
ENST00000374720108147702108147783In-frame

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Infer the effects of exon skipping event on protein functional features for SLC44A1

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000003747201052865710812862610812871016581741470498
ENST000003747201052865710813687810813701617421879498544
ENST000003747201052865710814540310814564018802116544623
ENST000003747201052865710814770210814778321172197623650

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000003747201052865710812862610812871016581741470498
ENST000003747201052865710813687810813701617421879498544
ENST000003747201052865710814540310814564018802116544623
ENST000003747201052865710814770210814778321172197623650

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q8WWI54704982657ChainID=PRO_0000191712;Note=Choline transporter-like protein 1
Q8WWI5470498474492Compositional biasNote=Cys-rich
Q8WWI5470498402537Topological domainNote=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI54985442657ChainID=PRO_0000191712;Note=Choline transporter-like protein 1
Q8WWI5498544402537Topological domainNote=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI5498544538558TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI55446232657ChainID=PRO_0000191712;Note=Choline transporter-like protein 1
Q8WWI5544623559566Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI5544623588653Topological domainNote=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI5544623538558TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI5544623567587TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI56236502657ChainID=PRO_0000191712;Note=Choline transporter-like protein 1
Q8WWI5623650644644Natural variantID=VAR_048837;Note=S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11698453;Dbxref=dbSNP:rs3199966,PMID:11698453
Q8WWI5623650588653Topological domainNote=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q8WWI54704982657ChainID=PRO_0000191712;Note=Choline transporter-like protein 1
Q8WWI5470498474492Compositional biasNote=Cys-rich
Q8WWI5470498402537Topological domainNote=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI54985442657ChainID=PRO_0000191712;Note=Choline transporter-like protein 1
Q8WWI5498544402537Topological domainNote=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI5498544538558TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI55446232657ChainID=PRO_0000191712;Note=Choline transporter-like protein 1
Q8WWI5544623559566Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI5544623588653Topological domainNote=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI5544623538558TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI5544623567587TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWI56236502657ChainID=PRO_0000191712;Note=Choline transporter-like protein 1
Q8WWI5623650644644Natural variantID=VAR_048837;Note=S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11698453;Dbxref=dbSNP:rs3199966,PMID:11698453
Q8WWI5623650588653Topological domainNote=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255


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SNVs in the skipped exons for SLC44A1

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.
SLC44A1_LUSC_exon_skip_497929_psi_boxplot.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A3A0-01exon_skip_497925
108118493108118662108118534108118534Frame_Shift_DelT-p.I181fs
STADTCGA-CG-4442-01exon_skip_497922
108097844108097980108097858108097858Nonsense_MutationTAp.L95*
STADTCGA-CG-4442-01exon_skip_497922
108097844108097980108097858108097858Nonsense_MutationTAp.L95X
UCECTCGA-AP-A056-01exon_skip_497925
108118493108118662108118629108118629Nonsense_MutationGTp.E213*
UCECTCGA-D1-A16X-01exon_skip_497925
108118493108118662108118629108118629Nonsense_MutationGTp.E213*
KIRCTCGA-B8-5553-01exon_skip_497929
108128627108128710108128708108128708Nonsense_MutationCTp.Q498X
LUSCTCGA-22-4613-01exon_skip_497929
108128627108128710108128711108128711Splice_SiteGTp.Q498_splice

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
SLC44A1_108127763_108127920_108128626_108128710_108136878_108137016_TCGA-22-4613-01Sample: TCGA-22-4613-01
Cancer type: LUSC
ESID: exon_skip_497929
Skipped exon start: 108128627
Skipped exon end: 108128710
Mutation start: 108128711
Mutation end: 108128711
Mutation type: Splice_Site
Reference seq: G
Mutation seq: T
AAchange: p.Q498_splice
exon_skip_49506_LUSC_TCGA-22-4613-01.png
boxplot
exon_skip_497929_LUSC_TCGA-22-4613-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
RL952_ENDOMETRIUM108097844108097980108097854108097854Frame_Shift_DelT-p.F94fs
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE108072005108072147108072026108072026Missense_MutationAGp.I50V
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE108072005108072147108072026108072026Missense_MutationAGp.I50V
BICR18_UPPER_AERODIGESTIVE_TRACT108072005108072147108072026108072026Missense_MutationAGp.I50V
LMSU_STOMACH108072005108072147108072143108072143Missense_MutationCTp.R89W
GP5D_LARGE_INTESTINE108097844108097980108097849108097849Missense_MutationTCp.V92A
LNCAPCLONEFGC_PROSTATE108097844108097980108097905108097905Missense_MutationGTp.A111S
SMSCTR_SOFT_TISSUE108136879108137016108136993108136993Missense_MutationGTp.D537Y
JHUEM7_ENDOMETRIUM108136879108137016108136996108136996Missense_MutationTGp.F538V
LS123_LARGE_INTESTINE108145404108145640108145411108145411Missense_MutationTCp.I547T
MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE108145404108145640108145585108145585Missense_MutationCTp.T605I
HEC1_ENDOMETRIUM108145404108145640108145603108145603Missense_MutationGAp.S611N
JHUEM7_ENDOMETRIUM108118493108118662108118629108118629Nonsense_MutationGTp.E213*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC44A1

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENST00000374724.1,ENST00000343170.7LGGrs3199966chr9:108147763T/G1.30e-03
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENST00000374724.1,ENST00000343170.7LGGrs3199966chr9:108147763T/G1.30e-03
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENST00000374724.1,ENST00000343170.7KIRCrs3199966chr9:108147763T/G1.50e-04
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENST00000374724.1,ENST00000343170.7KIRCrs3199966chr9:108147763T/G1.50e-04
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENST00000374724.1,ENST00000343170.7LUADrs3199966chr9:108147763T/G2.12e-03
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENST00000374724.1,ENST00000343170.7LUADrs3199966chr9:108147763T/G2.12e-03
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENST00000374724.1,ENST00000343170.7PAADrs3199966chr9:108147763T/G5.35e-05
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENST00000374724.1,ENST00000343170.7PAADrs3199966chr9:108147763T/G5.35e-05
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENST00000374724.1,ENST00000343170.7THCArs3199966chr9:108147763T/G3.36e-08
exon_skip_4979349108145403:108145640:108147702:108147783:108200561:108200782108147702:108147783ENST00000374724.1,ENST00000343170.7THCArs3199966chr9:108147763T/G3.37e-08
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENST00000470972.1,ENST00000374720.3LGGrs3199966chr9:108147763T/G1.30e-03
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENST00000470972.1,ENST00000374720.3LGGrs3199966chr9:108147763T/G1.30e-03
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENST00000470972.1,ENST00000374720.3KIRCrs3199966chr9:108147763T/G1.50e-04
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENST00000470972.1,ENST00000374720.3KIRCrs3199966chr9:108147763T/G1.50e-04
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENST00000470972.1,ENST00000374720.3LUADrs3199966chr9:108147763T/G2.12e-03
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENST00000470972.1,ENST00000374720.3LUADrs3199966chr9:108147763T/G2.12e-03
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENST00000470972.1,ENST00000374720.3PAADrs3199966chr9:108147763T/G5.35e-05
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENST00000470972.1,ENST00000374720.3PAADrs3199966chr9:108147763T/G5.35e-05
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENST00000470972.1,ENST00000374720.3THCArs3199966chr9:108147763T/G3.36e-08
exon_skip_4979339108145515:108145640:108147702:108147783:108151313:108151389108147702:108147783ENST00000470972.1,ENST00000374720.3THCArs3199966chr9:108147763T/G3.37e-08
exon_skip_4979129108061500:108061590:108062023:108062218:108072004:108072147108062023:108062218ENST00000607692.1COADrs2900397chr9:108062046G/A1.00e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC44A1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC44A1


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RelatedDrugs for SLC44A1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for SLC44A1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource