Homo sapiens gene SLC22A6, encoding solute carrier family 22 (organic anion transporter), member 6.
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SUMMARY back to top
RefSeq summary
[SLC22A6] The protein encoded by this gene is involved in the sodium-dependent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and may be localized to the basolateral membrane. Four transcript variants encoding four different isoforms have been found for this gene. [provided by RefSeq].

RefSeq annotates 4 representative transcripts (NM included in AceView variants .a, .b, .c and .d), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 5 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 1.2 times the average gene in this release. The sequence of this gene is defined by 145 GenBank accessions from 137 cDNA clones, some from kidney (seen 92 times), brain (8), cerebellum (4), pooled colon, kidney, stomach (2), whole brain (2), amygdala (once), caudate nucleus (once) and 7 other tissues. We annotate structural defects or features in 9 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 12 distinct gt-ag introns. Transcription produces 5 alternatively spliced mRNAs. There are 2 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, overlapping exons with different boundaries.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant cAug10, dAug10).
Function: There are 42 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Gout; Kidney Diseases) and proposed to participate in processes (alpha-ketoglutarate transport, organic anion transport, response to methotrexate, sodium-independent organic anion transport, transmembrane transport). Proteins are expected to have molecular functions (inorganic anion exchanger activity, organic anion transmembrane transporter activity, protein binding, sodium-independent organic anion transmembrane transporter activity) and to localize in various compartments (basolateral plasma membrane, integral to plasma membrane, caveola, membrane fraction, protein complex). A putative protein interactor has been described (APPBP2).
Protein coding potential: The 5 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (4 complete, 1 partial), some containing domains Major Facilitator Superfamily, Sugar (and other) transporter [Pfam], some transmembrane domains [Psort2].
2 isoforms are annotated using as Met a Kozak-compatible non-AUG start, thereby gaining a minimum of 81 amino acids N-terminal to the first AUG.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 11, links to other databases and other names
Map: This gene SLC22A6 maps on chromosome 11, at 11q12.3 according to Entrez Gene. In AceView, it covers 8.43 kb, from 62752494 to 62744064 (NCBI 37, August 2010), on the reverse strand.
Links to: the SNP view, gene overviews from Gene 9356, GeneCards, expression data from Gene 9356, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as SLC22A6, OAT1, PAHT, HOAT1, ROAT1, FLJ55736 or MGC45260, LOC9356. It has been described as solute carrier family 22 member 6, hPAHT, hROAT1, PAH transporter, organic anion transporter 1, para-aminohippurate transporter, renal organic anion transporter 1.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Slc22a6 (e=4 10-81).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes 3J974 (e=3 10-10), oct-1 (e=10-09), oat-1 (e=2 10-09), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene ATOCT4 (e=10-12), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
SLC22A6 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 262 4.71 0.42 32.8 99.3 0.24 3.57 3.57 20.2 0.14 0.19 426 0.63 0.78 0.11 140 0.17 8.19 5.79 0.21 0.11 0.55 1.45 0.18 1.45 852 2.05 0.06 0.29 0.07 5.04 0.59 524 0.09 0.34 3.57 10.8 0.89 0.22 0.27 524 2.70 0.22 0.15 28.5 0.22 3.33 323 0.13 0.18 0.78 0.16 2.19 0.10 80.7 0.08 0.12 0.45 8.78 0.12 323 0.10 0.18 0.11 0.42 0.68 0.78 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene SLC22A6 5' 3' encoded on minus strand of chromosome 11 from 62,752,494 to 62,744,064 411 400 341 376 489 438 582 4 15 a [NM] 411 400 341 376 489 438 582 4 815 b [NM] 411 400 341 376 489 438 582 513 15 c [NM] 411 400 341 376 489 438 582 513 815 d [NM] 1 341 376 489 e 1 2kb 0 676 bp exon 676 bp exon 274 bp [gt-ag] intron 58 GenBank accessions 353 RNA-seq supporting reads 287 Brain 21 Neuroblastoma 45 Other (also 6189 Primates bodymap) 104 bp exon 252 bp [gt-ag] intron 35 GenBank accessions 365 RNA-seq supporting reads 288 Brain 16 Neuroblastoma 61 Other (also 9741 Primates bodymap) 155 bp exon 1526 bp [gt-ag] intron 27 GenBank accessions 314 RNA-seq supporting reads 250 Brain 12 Neuroblastoma 52 Other (also 9158 Primates bodymap) 169 bp exon 458 bp [gt-ag] intron 21 GenBank accessions 355 RNA-seq supporting reads 1 UHR pooled cells 279 Brain 22 Neuroblastoma 53 Other (also 7809 Primates bodymap) 124 bp exon 159 bp [gt-ag] intron 20 GenBank accessions 469 RNA-seq supporting reads 1 UHR pooled cells 325 Brain 36 Neuroblastoma 107 Other (also 11294 Primates bodymap) 116 bp exon 1036 bp [gt-ag] intron 21 GenBank accessions 417 RNA-seq supporting reads 335 Brain 22 Neuroblastoma 60 Other (also 6387 Primates bodymap) 215 bp exon 137 bp [gt-ag] intron 25 GenBank accessions 557 RNA-seq supporting reads 456 Brain 29 Neuroblastoma 72 Other (also 9387 Primates bodymap) 109 bp exon 2232 bp [gt-ag] intron 4 GenBank accessions (also 99 Primates bodymap) 111 bp exon 263 bp [gt-ag] intron 4 GenBank accessions 11 RNA-seq supporting reads 2 Brain 9 Neuroblastoma 285 bp exon 53 accessions, NM_153278.1 some from kidney (seen 25 times) brain (6), cerebellum (4) pooled colon, kidney stomach (2), amygdala (once) 285 bp exon 676 bp exon 676 bp exon 274 bp [gt-ag] intron 58 GenBank accessions 353 RNA-seq supporting reads 287 Brain 21 Neuroblastoma 45 Other (also 6189 Primates bodymap) 104 bp exon 252 bp [gt-ag] intron 35 GenBank accessions 365 RNA-seq supporting reads 288 Brain 16 Neuroblastoma 61 Other (also 9741 Primates bodymap) 155 bp exon 1526 bp [gt-ag] intron 27 GenBank accessions 314 RNA-seq supporting reads 250 Brain 12 Neuroblastoma 52 Other (also 9158 Primates bodymap) 169 bp exon 458 bp [gt-ag] intron 21 GenBank accessions 355 RNA-seq supporting reads 1 UHR pooled cells 279 Brain 22 Neuroblastoma 53 Other (also 7809 Primates bodymap) 124 bp exon 159 bp [gt-ag] intron 20 GenBank accessions 469 RNA-seq supporting reads 1 UHR pooled cells 325 Brain 36 Neuroblastoma 107 Other (also 11294 Primates bodymap) 116 bp exon 1036 bp [gt-ag] intron 21 GenBank accessions 417 RNA-seq supporting reads 335 Brain 22 Neuroblastoma 60 Other (also 6387 Primates bodymap) 215 bp exon 137 bp [gt-ag] intron 25 GenBank accessions 557 RNA-seq supporting reads 456 Brain 29 Neuroblastoma 72 Other (also 9387 Primates bodymap) 109 bp exon 2232 bp [gt-ag] intron 4 GenBank accessions (also 99 Primates bodymap) 72 bp exon 302 bp [gt-ag] intron 29 GenBank accessions 786 RNA-seq supporting reads 638 Brain 46 Neuroblastoma 102 Other (also 14775 Primates bodymap) 285 bp exon 2 accessions, NM_153277.1 some from kidney (seen once) 285 bp exon 701 bp exon 701 bp exon 48 bp uORF 701 bp exon 701 bp exon 274 bp [gt-ag] intron 58 GenBank accessions 353 RNA-seq supporting reads 287 Brain 21 Neuroblastoma 45 Other (also 6189 Primates bodymap) 104 bp exon 104 bp exon 252 bp [gt-ag] intron 35 GenBank accessions 365 RNA-seq supporting reads 288 Brain 16 Neuroblastoma 61 Other (also 9741 Primates bodymap) 155 bp exon 155 bp exon 1526 bp [gt-ag] intron 27 GenBank accessions 314 RNA-seq supporting reads 250 Brain 12 Neuroblastoma 52 Other (also 9158 Primates bodymap) 169 bp exon 169 bp exon 458 bp [gt-ag] intron 21 GenBank accessions 355 RNA-seq supporting reads 1 UHR pooled cells 279 Brain 22 Neuroblastoma 53 Other (also 7809 Primates bodymap) 124 bp exon 124 bp exon 159 bp [gt-ag] intron 20 GenBank accessions 469 RNA-seq supporting reads 1 UHR pooled cells 325 Brain 36 Neuroblastoma 107 Other (also 11294 Primates bodymap) 116 bp exon 116 bp exon 1036 bp [gt-ag] intron 21 GenBank accessions 417 RNA-seq supporting reads 335 Brain 22 Neuroblastoma 60 Other (also 6387 Primates bodymap) 215 bp exon 215 bp exon 137 bp [gt-ag] intron 25 GenBank accessions 557 RNA-seq supporting reads 456 Brain 29 Neuroblastoma 72 Other (also 9387 Primates bodymap) 109 bp exon 109 bp exon 2100 bp [gt-ag] intron 24 GenBank accessions 489 RNA-seq supporting reads 397 Brain 31 Neuroblastoma 61 Other (also 8289 Primates bodymap) 243 bp exon 243 bp exon 263 bp [gt-ag] intron 4 GenBank accessions 11 RNA-seq supporting reads 2 Brain 9 Neuroblastoma 285 bp exon 285 bp exon 45 accessions, NM_004790.3 some from kidney (seen 44 times) capped 5' end, 42 accessions Validated 3' end, 1 accession 285 bp exon 676 bp exon 676 bp exon 48 bp uORF 676 bp exon 676 bp exon 274 bp [gt-ag] intron 58 GenBank accessions 353 RNA-seq supporting reads 287 Brain 21 Neuroblastoma 45 Other (also 6189 Primates bodymap) 104 bp exon 104 bp exon 252 bp [gt-ag] intron 35 GenBank accessions 365 RNA-seq supporting reads 288 Brain 16 Neuroblastoma 61 Other (also 9741 Primates bodymap) 155 bp exon 155 bp exon 1526 bp [gt-ag] intron 27 GenBank accessions 314 RNA-seq supporting reads 250 Brain 12 Neuroblastoma 52 Other (also 9158 Primates bodymap) 169 bp exon 169 bp exon 458 bp [gt-ag] intron 21 GenBank accessions 355 RNA-seq supporting reads 1 UHR pooled cells 279 Brain 22 Neuroblastoma 53 Other (also 7809 Primates bodymap) 124 bp exon 124 bp exon 159 bp [gt-ag] intron 20 GenBank accessions 469 RNA-seq supporting reads 1 UHR pooled cells 325 Brain 36 Neuroblastoma 107 Other (also 11294 Primates bodymap) 116 bp exon 116 bp exon 1036 bp [gt-ag] intron 21 GenBank accessions 417 RNA-seq supporting reads 335 Brain 22 Neuroblastoma 60 Other (also 6387 Primates bodymap) 215 bp exon 215 bp exon 137 bp [gt-ag] intron 25 GenBank accessions 557 RNA-seq supporting reads 456 Brain 29 Neuroblastoma 72 Other (also 9387 Primates bodymap) 109 bp exon 109 bp exon 2100 bp [gt-ag] intron 24 GenBank accessions 489 RNA-seq supporting reads 397 Brain 31 Neuroblastoma 61 Other (also 8289 Primates bodymap) 204 bp exon 204 bp exon 302 bp [gt-ag] intron 29 GenBank accessions 786 RNA-seq supporting reads 638 Brain 46 Neuroblastoma 102 Other (also 14775 Primates bodymap) 285 bp exon 285 bp exon 28 accessions, NM_153276.1 some from kidney (seen 12 times) brain (2), whole brain (2) colon, kidney, stomach adult, whole pooled (once) eye (once) capped 5' end, 2 accessions Validated 3' end, 10 accessions 285 bp exon 124 bp exon 124 bp exon 78 bp [gt-ag] intron 1 GenBank accession (also 4 Primates bodymap) 155 bp exon 1526 bp [gt-ag] intron 27 GenBank accessions 314 RNA-seq supporting reads 250 Brain 12 Neuroblastoma 52 Other (also 9158 Primates bodymap) 169 bp exon 458 bp [gt-ag] intron 21 GenBank accessions 355 RNA-seq supporting reads 1 UHR pooled cells 279 Brain 22 Neuroblastoma 53 Other (also 7809 Primates bodymap) 124 bp exon 159 bp [gt-ag] intron 20 GenBank accessions 469 RNA-seq supporting reads 1 UHR pooled cells 325 Brain 36 Neuroblastoma 107 Other (also 11294 Primates bodymap) 1 accession from kidney 90 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top


Click on the headers to reorder the lines
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aAug10 2064 bp 599 aa 67 bp 197 bp   2kb probably including promoter 8401 bp 1kb
bAug10 2025 bp 586 aa 67 bp 197 bp   2kb probably including promoter 8401 bp 1kb
cAug10 2221 bp 563 aa 332 bp 197 bp 45 bp 2kb including Promoter 8426 bp 1kb
dAug10 2157 bp 550 aa 307 bp 197 bp 45 bp 2kb including Promoter 8401 bp 1kb
eAug10 662 bp 220 aa       2kb 2883 bp 1kb
Gene neighbors and Navigator on chromosome 11q12.3 back to top
R ROM1 D C I R P METTL12andSNORA57 C R P C11orf83 R P R GNG3 D I R P TTC9C C R P POLR2G D C I R P TAF6L C I R P TMEM179B C R P R R SLC3A2 D C I R P R SLC22A10andSLC22A9 C I R P CCND2P P D C I R P TUT1andEEF1G D C I R P MTA2 C I R P EML3 C I R P B3GAT3 D C I R P GANAB C R P C11orf48andINTS5 C I R P UBXN1 C R LRRN4CL D C I R P HNRNPUL2andBSCL2 C I R ZBTB3 C I R P NXF1andTMEM223 D C I R P STX5 C I R P RNU2-2andWDR74 R P SNHG1_ D C I R P CHRM1 D C I R P SLC22A6 C R P SLC22A8 C C I R P SLC22A24 C R P SLC22A25 100kb 0 peeskeyby, 1 accession ROM1, 131 accessions, 4 variants METTL12andSNORA57, 74 accessions 5 variants C11orf83, 90 accessions 4 variants zaflobu, 10 accessions 2 variants GNG3, 104 accessions, 2 variants TTC9C, 162 accessions 13 variants POLR2G, 447 accessions 11 variants TAF6L, 277 accessions 11 variants TMEM179B, 156 accessions 8 variants fawferby, 3 accessions 2 variants tarkarby, 12 accessions 4 variants SLC3A2, 791 accessions 34 variants glermer, 1 accession SLC22A10andSLC22A9, 83 accessions 13 variants CCND2P, 1 accession poykoby, 1 accession jarmuby, 2 accessions joymuby, 1 accession klustaby, 1 accession smawglaw, 1 accession kamuby, 1 accession klawstaby, 1 accession klerstaby, 1 accession hesemi, 40 accessions pleestaby, 3 accessions komuby, 1 accession farplar, 1 accession foyplar, 1 accession guplar, 3 accessions geeplar, 1 accession kawmuby, 1 accession lerglobu, 1 accession leyglobu, 1 accession loyglobu, 12 accessions skeestaby, 1 accession luplar, 2 accessions lymuby, 2 accessions larmuby, 1 accession rerplar, 1 accession slostaby, 2 accessions mamuby, 4 accessions mawmuby, 1 accession meyglobu, 4 accessions meemuby, 2 accessions meymuby, 1 accession sloystaby, 1 accession morglobu, 1 accession narmuby, 6 accessions neemuby, 3 accessions neymuby, 1 accession smorna, 8 accessions sherkoby, 3 accessions waplar, 1 accession blatobo, 1 accession pormuby, 1 accession hosemi, 2 accessions stastaby, 1 accession zyflobu, 5 accessions norglobu, 1 accession noyglobu, 1 accession pyglobu, 1 accession puglobu, 1 accession sterstaby, 1 accession rermuby, 1 accession poyglobu, 1 accession zawplar, 2 accessions ryglobu, 1 accession lawfaw, 12 accessions flustaby, 1 accession flarstaby, 1 accession fleestaby, 1 accession fleystaby, 1 accession glustaby, 1 accession glawstaby, 1 accession gleystaby, 4 accessions klostaby, 1 accession klarstaby, 1 accession plustaby, 5 accessions reykoby, 1 accession lawglobu, 1 accession sakoby, 1 accession lorglobu, 2 accessions marglobu, 1 accession gerplar, 1 accession vorkoby, 3 accessions gorplar, 1 accession meeglobu, 1 accession loplar, 1 accession slystaby, 1 accession sporfeeby, 1 accession slarstaby, 5 accessions saplar, 1 accession slorstaby, 1 accession nermuby, 1 accession moyglobu, 1 accession naglobu, 2 accessions smerstaby, 1 accession nyglobu, 1 accession mihiro, 1 accession snustaby, 1 accession noglobu, 1 accession spostaby, 1 accession pawmuby, 1 accession sparstaby, 1 accession narglobu, 1 accession peymuby, 1 accession sperstaby, 1 accession ramuby, 1 accession rymuby, 3 accessions romuby, 1 accession rarmuby, 1 accession weyplar, 2 accessions rawmuby, 1 accession neyglobu, 1 accession plorchoy, 3 accessions parglobu, 1 accession zaplar, 2 accessions reemuby, 2 accessions AHNAK, 456 accessions 11 variants TUT1andEEF1G, 586 accessions 23 variants MTA2, 125 accessions, 8 variants EML3, 246 accessions, 16 variants B3GAT3, 374 accessions 9 variants GANAB, 573 accessions 30 variants C11orf48andINTS5, 468 accessions 16 variants UBXN1, 375 accessions 19 variants LRRN4CL, 55 accessions HNRNPUL2andBSCL2, 994 accessions 33 variants ZBTB3, 34 accessions, 4 variants NXF1andTMEM223, 539 accessions 28 variants STX5, 419 accessions, 18 variants RNU2-2andWDR74, 365 accessions 21 variants SNHG1_, 766 accessions 46 variants CHRM1, 197 accessions 3 variants SLC22A6, 138 accessions 5 variants SLC22A8, 147 accessions 12 variants gleymer, 2 accessions SLC22A24, 19 accessions 2 variants SLC22A25, 35 accessions 9 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               42 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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