Homo sapiens gene RPS6KA3, encoding ribosomal protein S6 kinase, 90kDa, polypeptide 3.
SUMMARY back to top
RefSeq summary
[RPS6KA3] This gene encodes a member of the RSK (ribosomal S6 kinase) family of serine/threonine kinases. This kinase contains 2 non-identical kinase catalytic domains and phosphorylates various substrates, including members of the mitogen-activated kinase (MAPK) signalling pathway. The activity of this protein has been implicated in controlling cell growth and differentiation. Mutations in this gene have been associated with Coffin-Lowry syndrome (CLS). [provided by RefSeq].

RefSeq annotates one representative transcript (NM included in AceView variant.b), 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 11 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 3.0 times the average gene in this release. The sequence of this gene is defined by 344 GenBank accessions from 319 cDNA clones, some from liver and spleen (seen 20 times), liver (12), lung (11), prostate (11), stomach (10), kidney (9), skin (9) and 113 other tissues. We annotate structural defects or features in 14 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 33 distinct gt-ag introns. Transcription produces 19 different mRNAs, 11 alternatively spliced variants and 8 unspliced forms. There are 4 probable alternative promotors, 3 non overlapping alternative last exons and 8 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 3 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron.
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).
Function: There are 88 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: Coffin-Lowry syndrome; Other sources: Abnormalities, Multiple; Ataxia Telangiectasia; Carcinoma; Cell Transformation, Neoplastic; Diabetes mellitus, type 2; Mental Retardation; Mental retardation, X-linked nonspecific, type 19; Prostatic Neoplasms; Syndrome), proposed to participate in pathways (Long-term potentiation, MAPK signaling pathway, MAPKinase Signaling Pathway, mTOR signaling pathway, Neurotrophin signaling pathway, Oocyte meiosis, Progesterone-mediated oocyte maturation, Signaling Pathway from G-Protein Families) and processes (intracellular protein kinase cascade, protein amino acid phosphorylation). Proteins are expected to have molecular functions (ATP binding, magnesium ion binding, nucleotide binding, transferase activity) and to localize in various compartments (cytoplasm, membrane). Putative protein interactors have been described (BAD, CREB1, CREBBP, ESR1, FGF2, GRIN1, GRIN2D, HIST3H3, HMGN1, HMGN2, HTR2A, KRT18, MAGI1, MAPK1, MAPK3, MAPK14, MAPT, METTL1, NR4A1, PDPK1, PEA15, RPS6KA3, SHANK1, STK11).
Protein coding potential: 9 spliced mRNAs putatively encode good proteins, altogether 9 different isoforms (5 complete, 2 COOH complete, 2 partial), some containing domains Protein kinase domain, Protein kinase C terminal domain, Protein tyrosine kinase [Pfam], some transmembrane domains [Psort2]. The remaining 10 mRNA variants (2 spliced, 8 unspliced; 7 partial) appear not to encode good proteins.
Isoform RPS6KA3.aAug10 is annotated using as Met a Kozak-compatible g..GTGg start, thereby gaining 126 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by acetylation; mono-methylation; 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 X, links to other databases and other names
Map: This gene RPS6KA3 maps on chomosome X at position +302.03 (interpolated), at Xp22.2-p22.1 according to Entrez Gene. In AceView, it covers 117.50 kb, from 20285523 to 20168025 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from OMIM_303600, KEGG_04010, KEGG_04114, KEGG_04150, KEGG_04720, KEGG_04722, KEGG_04914, PhosphoSite, the SNP view, gene overviews from Entrez Gene 6197, 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 RPS6KA3, RP11-393H10.3, CLS, RSK, HU-3, RSK2, MRX19, ISPK-1, p90-RSK2, pp90RSK2, MAPKAPK1B, S6K-alpha3, LOC6197 or spymoy, pawfee. It has been described as ribosomal protein S6 kinase alpha-3, RSK-2, p90RSK3, p90-RSK 3, MAPKAPK-1b, S6K-alpha-3, MAPKAP kinase 1b, ribosomal S6 kinase 2, mental retardation, X-linked 19, MAPK-activated protein kinase 1b, insulin-stimulated protein kinase 1, 90 kDa ribosomal protein S6 kinase 3, MAP kinase-activated protein kinase 1b.
EC number: This gene encodes protein number:
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Rps6ka3 (e=0.0).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene rskn-1 (e= 10-136), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes ATPK19 (e=10-75), ATPK1 (e=10-75), 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
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!.
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
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.
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 uORF Upstream sequence Transcription
Downstream sequence
aAug10 3641 bp 864 aa 26 bp 1020 bp 2kb possibly including promoter 112656 bp 1kb
bAug10 7712 bp 740 aa 5486 bp 2kb including Promoter 116724 bp 1kb
cAug10 3054 bp 712 aa 483 bp 432 bp 57 bp 2kb possibly including promoter 112440 bp 1kb
dAug10 2451 bp 711 aa 174 bp 141 bp 2kb possibly including promoter 111810 bp 1kb
eAug10 2508 bp 710 aa 121 bp 254 bp 2kb possibly including promoter 63816 bp 1kb
fAug10 1088 bp 337 aa 76 bp 2kb including Promoter 90850 bp 1kb
gAug10 823 bp 273 aa 2kb 17400 bp 1kb
hAug10 2047 bp 206 aa 1426 bp 2kb 15150 bp 1kb
iAug10 918 bp 95 aa 628 bp 2kb 15497 bp 1kb
jAug10-unspliced 1096 bp 58 aa 922 bp 2kb 1096 bp 1kb
kAug10-unspliced 1012 bp 67 aa 371 bp 437 bp 2kb 1012 bp 1kb
lAug10-unspliced 854 bp 64 aa 657 bp 2kb 854 bp 1kb
mAug10-unspliced 828 bp 57 aa 371 bp 283 bp 2kb 828 bp 1kb
nAug10-unspliced 771 bp 86 aa 509 bp 2kb 771 bp 1kb
oAug10 585 bp 65 aa 388 bp 2kb 62035 bp 1kb
pAug10-unspliced 584 bp 68 aa 375 bp 2kb 584 bp 1kb
qAug10 528 bp 86 aa 268 bp 2kb 71970 bp 1kb
rAug10-unspliced 502 bp 41 aa 77 bp 299 bp 2kb 502 bp 1kb
sAug10-unspliced 433 bp 76 aa 202 bp 2kb 433 bp 1kb

Gene neighbors and Navigator on chromosome Xp22.2-p22.1 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications        
Annotated mRNA diagrams back to top
Bibliography:               88 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j-u, .k-u, .l-u, .m-u, .n-u, .o, .p-u, .q, .r-u, .s-u 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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