Homo sapiens gene SLC6A11, encoding solute carrier family 6 (neurotransmitter transporter, GABA), member 11.
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SUMMARY back to top
RefSeq summary
[SLC6A11] Gamma-aminobutyric acid (GABA) is a major inhibitory neurotransmitter. GABAergic neurotransmission is terminated by the uptake of GABA into the presynaptic terminal and the surrounding astroglial cells by sodium-dependent transporters, such as SLC6A11.[supplied by OMIM].

RefSeq annotates one representative transcript (NM included in AceView variant.a), 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 3 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 0.5 times the average gene in this release. The sequence of this gene is defined by 63 GenBank accessions from 54 cDNA clones, some from brain (seen 7 times), whole brain (4), liver (2), testis (2), blastocyst (once), brain, hypothalamus (once), cerebellum (once) and 11 other tissues.
Alternative mRNA variants and regulation: The gene contains 13 distinct gt-ag introns. Transcription produces 4 different mRNAs, 3 alternatively spliced variants and 1 unspliced form. There are 3 non overlapping alternative last exons and 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end.
Function: There are 8 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to a disease (Disease Models, Animal) and proposed to participate in a process (neurotransmitter transport). Proteins are expected to have molecular functions (gamma-aminobutyric acid:sodium symporter activity, neurotransmitter binding, neurotransmitter:sodium symporter activity) and to localize in various compartments (integral to membrane, plasma membrane, integral to plasma membrane).
Protein coding potential: 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 COOH complete), some containing Sodium:neurotransmitter symporter family domain [Pfam], some transmembrane domains [Psort2]. The remaining mRNA variant (unspliced) appears not to encode a good protein. Finally proteins from this gene may be modulated by acetylation; phosphorylation; ubiquitination, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 3, links to other databases and other names
Map: This gene SLC6A11 maps on chromosome 3, at 3p25.3 according to Entrez Gene. In AceView, it covers 123.01 kb, from 10857886 to 10980890 (NCBI 37, August 2010), on the direct strand.
Links to: , manual annotations from GAD, PhosphoSite, the SNP view, gene overviews from Entrez Gene 6538, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as SLC6A11, GAT3, GAT4 or GAT-3, LOC6538. It has been described as sodium- and chloride-dependent GABA transporter 3, solute carrier family 6 member 11.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Slc6a11 (e=0.0).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene snf-11 (e= 10-162), 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
SLC6A11 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 0.24 2.90 20.2 0.06 0.13 2.70 4.39 10.1 16.4 0.45 5.04 1.91 16.4 21.6 16.4 6.65 9.41 0.11 0.10 5.40 17.6 75.3 1.91 0.17 0.42 0.08 0.39 0.45 99.3 6.65 0.12 0.11 0.09 0.19 7.13 2.35 2.35 0.10 0.63 0.59 0.21 0.07 0.09 9.41 0.15 0.14 1.18 0.12 2.19 0.12 0.09 1.55 20.2 17.6 1.45 0.09 1.55 13.3 0.09 0.11 0.83 0.68 131 0.22 0.18 0.19 0.08 1.91 0.21 0.48 11.6 0.15 0.21 1.66 15.3 0.32 0.10 3.33 0.24 1.45 14.3 1.78 0.07 2.19 0.13 0.27 1.02 0.13 30.6 0.24 0.22 12.4 1.55 15.3 1.66 0.13 0.27 0.55 0.42 7.13 16.4 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 SLC6A11 5' 3' encoded on plus strand of chromosome 3 from 10,857,886 to 10,980,890 5011 9250 6369 5973 4687 4951 4202 3799 4462 4849 5307 5314 6853 a [NM] 5011 9250 6369 b 5314 c d-u 1 2kb 0 321 bp exon 321 bp exon 2943 bp [gt-ag] intron 19 GenBank accessions 4992 RNA-seq supporting reads 668 UHR pooled cells 2653 Brain 1531 Neuroblastoma 140 Other (also 2082 Primates bodymap) 135 bp exon 112 bp [gt-ag] intron 19 GenBank accessions 9231 RNA-seq supporting reads 1351 UHR pooled cells 5038 Brain 2566 Neuroblastoma 276 Other (also 4114 Primates bodymap) 141 bp exon 3449 bp [gt-ag] intron 13 GenBank accessions 6356 RNA-seq supporting reads 849 UHR pooled cells 3464 Brain 1868 Neuroblastoma 175 Other (also 2808 Primates bodymap) 91 bp exon 20821 bp [gt-ag] intron 5 GenBank accessions 5968 RNA-seq supporting reads 786 UHR pooled cells 3493 Brain 1554 Neuroblastoma 135 Other (also 1942 Primates bodymap) 133 bp exon 30614 bp [gt-ag] intron 3 GenBank accessions 4684 RNA-seq supporting reads 587 UHR pooled cells 2727 Brain 1258 Neuroblastoma 112 Other (also 2127 Primates bodymap) 135 bp exon 36994 bp [gt-ag] intron 9 GenBank accessions 4942 RNA-seq supporting reads 639 UHR pooled cells 2881 Brain 1293 Neuroblastoma 129 Other (also 1651 Primates bodymap) 104 bp exon 6135 bp [gt-ag] intron 14 GenBank accessions 4188 RNA-seq supporting reads 516 UHR pooled cells 2482 Brain 4 Blood 1061 Neuroblastoma 125 Other (also 1278 Primates bodymap) 125 bp exon 7551 bp [gt-ag] intron 14 GenBank accessions 3785 RNA-seq supporting reads 445 UHR pooled cells 2438 Brain 1 Blood 795 Neuroblastoma 106 Other (also 1464 Primates bodymap) 113 bp exon 3085 bp [gt-ag] intron 15 GenBank accessions 4447 RNA-seq supporting reads 546 UHR pooled cells 2908 Brain 2 Blood 896 Neuroblastoma 95 Other (also 1675 Primates bodymap) 138 bp exon 3811 bp [gt-ag] intron 19 GenBank accessions 4830 RNA-seq supporting reads 588 UHR pooled cells 3116 Brain 2 Blood 956 Neuroblastoma 168 Other (also 1541 Primates bodymap) 103 bp exon 812 bp [gt-ag] intron 18 GenBank accessions 5289 RNA-seq supporting reads 587 UHR pooled cells 3567 Brain 954 Neuroblastoma 181 Other (also 1863 Primates bodymap) 101 bp exon 862 bp [gt-ag] intron 21 GenBank accessions 5293 RNA-seq supporting reads 575 UHR pooled cells 3414 Brain 1 Blood 1084 Neuroblastoma 219 Other (also 1813 Primates bodymap) 171 bp exon 3050 bp [gt-ag] intron 7 GenBank accessions 6846 RNA-seq supporting reads 769 UHR pooled cells 4630 Brain 8 Blood 1242 Neuroblastoma 197 Other (also 1936 Primates bodymap) 955 bp exon 49 accessions, NM_014229.1 some from brain (seen 6 times) whole brain (4), liver (2) blastocyst (once), cerebellum (once) capped 5' end, 5 accessions Validated 3' end, 1 accession Validated 3' end, 4 accessions 955 bp exon 321 bp exon 321 bp exon 2943 bp [gt-ag] intron 19 GenBank accessions 4992 RNA-seq supporting reads 668 UHR pooled cells 2653 Brain 1531 Neuroblastoma 140 Other (also 2082 Primates bodymap) 135 bp exon 112 bp [gt-ag] intron 19 GenBank accessions 9231 RNA-seq supporting reads 1351 UHR pooled cells 5038 Brain 2566 Neuroblastoma 276 Other (also 4114 Primates bodymap) 141 bp exon 3449 bp [gt-ag] intron 13 GenBank accessions 6356 RNA-seq supporting reads 849 UHR pooled cells 3464 Brain 1868 Neuroblastoma 175 Other (also 2808 Primates bodymap) 2197 bp exon 4 accessions, some from brain (seen once) brain, hypothalamus (once) frontal lobe (once), testis (once) Validated 3' end, 1 accession 2197 bp exon 206 bp exon 206 bp exon 862 bp [gt-ag] intron 21 GenBank accessions 5293 RNA-seq supporting reads 575 UHR pooled cells 3414 Brain 1 Blood 1084 Neuroblastoma 219 Other (also 1813 Primates bodymap) 369 bp exon 1 accession from head neck 369 bp exon 605 bp exon 605 bp exon 1 accession 605 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
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 2766 bp 632 aa 65 bp 802 bp 2kb including Promoter 123005 bp 1kb
bAug10 2794 bp 208 aa 65 bp 2102 bp 2kb probably including promoter 9298 bp 1kb
cAug10 575 bp 188 aa 6 bp 2kb 1437 bp 1kb
dAug10-unspliced 605 bp 83 aa 33 bp 320 bp 2kb 605 bp 1kb

Gene neighbors and Navigator on chromosome 3p25.3 back to top
SLC6A11 C R P R R SLC6A1 D C I R P HRH1 D C R P D C I R P ATP2B2 G R R R 100kb 0 SLC6A11, 55 accessions 4 variants tamora, 12 accessions smudawbo, 30 accessions SLC6A1, 137 accessions 6 variants HRH1, 103 accessions, 7 variants ATG7, 317 accessions, 33 variants pludawbo, 1 accession blarveebo, 1 accession plardawbo, 1 accession pleedawbo, 1 accession plerdawbo, 2 accessions pleydawbo, 1 accession neyumo, 2 accessions, 2 variants ploydawbo, 1 accession skydawbo, 1 accession skodawbo, 2 accessions skardawbo, 1 accession skawdawbo, 1 accession skerdawbo, 1 accession nawfaw, 2 accessions skordawbo, 1 accession slydawbo, 4 accessions slodawbo, 1 accession slardawbo, 1 accession sleedawbo, 1 accession choysparby, 2 accessions sloydawbo, 1 accession keruyo, 1 accession smodawbo, 1 accession smawdawbo, 1 accession smeedawbo, 1 accession smerdawbo, 1 accession smordawbo, 2 accessions snudawbo, 1 accession snardawbo, 2 accessions snawdawbo, 1 accession snerdawbo, 1 accession sneydawbo, 2 accessions snordawbo, 1 accession sposwoybu, 2 accessions spudawbo, 1 accession noyumo, 3 accessions, 2 variants speedawbo, 2 accessions speydawbo, 3 accessions blawsparby, 1 accession stydawbo, 1 accession barjubo, 1 accession stardawbo, 8 accessions flasparby, 1 accession sterdawbo, 1 accession steydawbo, 2 accessions stordawbo, 1 accession swudawbo, 1 accession swodawbo, 1 accession swawdawbo, 1 accession bawjubo, 1 accession swoydawbo, 1 accession badeebo, 1 accession budeebo, 1 accession timora, 1 accession bodeebo, 1 accession beedeebo, 1 accession berdeebo, 1 accession bordeebo, 1 accession gloysparby, 1 accession dodeebo, 1 accession klysparby, 2 accessions dawdeebo, 1 accession deedeebo, 1 accession derdeebo, 1 accession dordeebo, 2 accessions beyjubo, 1 accession fadeebo, 1 accession fydeebo, 1 accession fudeebo, 1 accession fawdeebo, 1 accession feedeebo, 1 accession tayumo, 1 accession ferdeebo, 4 accessions foydeebo, 1 accession gadeebo, 3 accessions kleedawbo, 4 accessions bloveebo, 1 accession kleydawbo, 1 accession klordawbo, 1 accession zosparby, 1 accession swoyjybo, 1 accession plydawbo, 2 accessions plawdawbo, 1 accession kuruyo, 1 accession plordawbo, 1 accession skadawbo, 1 accession skudawbo, 5 accessions skeedawbo, 3 accessions skeydawbo, 1 accession skoydawbo, 1 accession bajubo, 1 accession slawdawbo, 1 accession smeydawbo, 5 accessions smoydawbo, 5 accessions 4 variants snydawbo, 2 accessions sheysparby, 1 accession bujubo, 1 accession spadawbo, 1 accession spydawbo, 1 accession spardawbo, 1 accession noyfaw, 3 accessions spawdawbo, 2 accessions sperdawbo, 3 accessions spoydawbo, 2 accessions studawbo, 1 accession stodawbo, 4 accessions steedawbo, 1 accession stoydawbo, 2 accessions swadawbo, 1 accession swydawbo, 2 accessions swardawbo, 1 accession sweedawbo, 1 accession sweydawbo, 1 accession swordawbo, 1 accession bydeebo, 1 accession beydeebo, 2 accessions boydeebo, 1 accession dadeebo, 1 accession dydeebo, 2 accessions deydeebo, 5 accessions beejubo, 2 accessions doydeebo, 2 accessions fardeebo, 1 accession feydeebo, 1 accession fordeebo, 1 accession ATP2B2, 196 accessions 8 variants LOC285370, 10 accessions 2 variants zorswerby, 14 accessions 3 variants zoyswerby, 6 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               8 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !