Human Gene RPS6KA4 (ENST00000334205.9_9) from GENCODE V47lift37
  Description: ribosomal protein S6 kinase A4, transcript variant 1 (from RefSeq NM_003942.3)
Gencode Transcript: ENST00000334205.9_9
Gencode Gene: ENSG00000162302.13_12
Transcript (Including UTRs)
   Position: hg19 chr11:64,126,634-64,139,687 Size: 13,054 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr11:64,126,708-64,138,952 Size: 12,245 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:64,126,634-64,139,687)mRNA (may differ from genome)Protein (772 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: KS6A4_HUMAN
DESCRIPTION: RecName: Full=Ribosomal protein S6 kinase alpha-4; Short=S6K-alpha-4; EC=2.7.11.1; AltName: Full=90 kDa ribosomal protein S6 kinase 4; AltName: Full=Nuclear mitogen- and stress-activated protein kinase 2; AltName: Full=Ribosomal protein kinase B; Short=RSKB;
FUNCTION: Serine/threonine-protein kinase that is required for the mitogen or stress-induced phosphorylation of the transcription factors CREB1 and ATF1 and for the regulation of the transcription factor RELA, and that contributes to gene activation by histone phosphorylation and functions in the regulation of inflammatory genes. Phosphorylates CREB1 and ATF1 in response to mitogenic or stress stimuli such as UV-C irradiation, epidermal growth factor (EGF) and anisomycin. Plays an essential role in the control of RELA transcriptional activity in response to TNF. Phosphorylates 'Ser-10' of histone H3 in response to mitogenics, stress stimuli and EGF, which results in the transcriptional activation of several immediate early genes, including proto-oncogenes c-fos/FOS and c-jun/JUN. May also phosphorylate 'Ser-28' of histone H3. Mediates the mitogen- and stress-induced phosphorylation of high mobility group protein 1 (HMGN1/HMG14). In lipopolysaccharide- stimulated primary macrophages, acts downstream of the Toll-like receptor TLR4 to limit the production of pro-inflammatory cytokines. Functions probably by inducing transcription of the MAP kinase phosphatase DUSP1 and the anti-inflammatory cytokine interleukin 10 (IL10), via CREB1 and ATF1 transcription factors.
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
COFACTOR: Magnesium.
ENZYME REGULATION: Activated by phosphorylation at Ser-343, Thr- 568 and Thr-687 by MAPK1/ERK2, MAPK3/ERK1 and MAPK14/p38-alpha, and by further autophosphorylation of Ser-196, Ser-360 and Ser-365 by the activated C-terminal kinase domain (By similarity).
SUBUNIT: Forms a complex with either MAPK1/ERK2 or MAPK3/ERK1 in quiescent cells which transiently dissociates following mitogenic stimulation. Also associates with MAPK14/p38-alpha. Activated RPS6KA4 associates with and phosphorylates the NF-kappa-B p65 subunit RELA.
INTERACTION: Q16539:MAPK14; NbExp=2; IntAct=EBI-73933, EBI-73946;
SUBCELLULAR LOCATION: Nucleus.
PTM: Ser-343 and Thr-568 phosphorylation is required for kinase activity. Ser-343 and Ser-196 are autophosphorylated by the C- terminal kinase domain, and their phosphorylation is essential for the catalytic activity of the N-terminal kinase domain. Phosphorylated at Ser-343, Thr-568 and Thr-687 by MAPK1/ERK2, MAPK3/ERK1 and MAPK14/p38-alpha. Autophosphorylated at Ser-737 and Ser-745 by the N-terminal kinase domain (By similarity).
MISCELLANEOUS: Enzyme activity requires the presence of both kinase domains (By similarity).
SIMILARITY: Belongs to the protein kinase superfamily. AGC Ser/Thr protein kinase family. S6 kinase subfamily.
SIMILARITY: Contains 1 AGC-kinase C-terminal domain.
SIMILARITY: Contains 2 protein kinase domains.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 50.93 RPKM in Brain - Cerebellum
Total median expression: 694.12 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 -33.0074-0.446 Picture PostScript Text
3' UTR -329.40735-0.448 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
IPR000961 - AGC-kinase_C
IPR011009 - Kinase-like_dom
IPR017892 - Pkinase_C
IPR000719 - Prot_kinase_cat_dom
IPR017441 - Protein_kinase_ATP_BS
IPR016239 - Ribosomal_S6_kinase_II
IPR002290 - Ser/Thr_dual-sp_kinase_dom
IPR008271 - Ser/Thr_kinase_AS

Pfam Domains:
PF00069 - Protein kinase domain
PF00433 - Protein kinase C terminal domain
PF01163 - RIO1 family
PF07714 - Protein tyrosine and serine/threonine kinase

SCOP Domains:
56112 - Protein kinase-like (PK-like)

ModBase Predicted Comparative 3D Structure on O75676
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004711 ribosomal protein S6 kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0001818 negative regulation of cytokine production
GO:0006355 regulation of transcription, DNA-templated
GO:0006468 protein phosphorylation
GO:0006954 inflammatory response
GO:0016310 phosphorylation
GO:0016572 histone phosphorylation
GO:0032793 positive regulation of CREB transcription factor activity
GO:0033129 positive regulation of histone phosphorylation
GO:0035066 positive regulation of histone acetylation
GO:0035556 intracellular signal transduction
GO:0043987 histone H3-S10 phosphorylation
GO:0043988 histone H3-S28 phosphorylation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0070498 interleukin-1-mediated signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF212765 - JP 2014500723-A/20268: Polycomb-Associated Non-Coding RNAs.
LF211202 - JP 2014500723-A/18705: Polycomb-Associated Non-Coding RNAs.
AK223561 - Homo sapiens mRNA for ribosomal protein S6 kinase, 90kDa, polypeptide 4 isoform b variant, clone: FCC127G11.
AJ010119 - Homo sapiens mRNA for Ribosomal protein kinase B (RSK-B).
AK292163 - Homo sapiens cDNA FLJ78603 complete cds, highly similar to Homo sapiens ribosomal protein S6 kinase, 90kDa, polypeptide 4 (RPS6KA4), transcript variant 1, mRNA.
AK313567 - Homo sapiens cDNA, FLJ94131.
BC047896 - Homo sapiens ribosomal protein S6 kinase, 90kDa, polypeptide 4, mRNA (cDNA clone MGC:57704 IMAGE:5763859), complete cds.
AK298507 - Homo sapiens cDNA FLJ51927 complete cds, highly similar to Ribosomal protein S6 kinase alpha-4 (EC 2.7.11.1).
BC028079 - Homo sapiens ribosomal protein S6 kinase, 90kDa, polypeptide 4, mRNA (cDNA clone IMAGE:5216639), partial cds.
CU690526 - Synthetic construct Homo sapiens gateway clone IMAGE:100021480 5' read RPS6KA4 mRNA.
KJ901930 - Synthetic construct Homo sapiens clone ccsbBroadEn_11324 RPS6KA4 gene, encodes complete protein.
KJ905364 - Synthetic construct Homo sapiens clone ccsbBroadEn_14920 RPS6KA4 gene, encodes complete protein.
AF074715 - Homo sapiens mitogen- and stress-activated protein kinase-2 (MSK2) mRNA, partial cds.
LF344594 - JP 2014500723-A/152097: Polycomb-Associated Non-Coding RNAs.
BC020451 - Homo sapiens ribosomal protein S6 kinase, 90kDa, polypeptide 4, mRNA (cDNA clone IMAGE:3449605).
LF344593 - JP 2014500723-A/152096: Polycomb-Associated Non-Coding RNAs.
LF344591 - JP 2014500723-A/152094: Polycomb-Associated Non-Coding RNAs.
LF344590 - JP 2014500723-A/152093: Polycomb-Associated Non-Coding RNAs.
JD247347 - Sequence 228371 from Patent EP1572962.
LF344589 - JP 2014500723-A/152092: Polycomb-Associated Non-Coding RNAs.
JD553323 - Sequence 534347 from Patent EP1572962.
JD217128 - Sequence 198152 from Patent EP1572962.
LF344588 - JP 2014500723-A/152091: Polycomb-Associated Non-Coding RNAs.
JD252453 - Sequence 233477 from Patent EP1572962.
JD062666 - Sequence 43690 from Patent EP1572962.
LF344587 - JP 2014500723-A/152090: Polycomb-Associated Non-Coding RNAs.
JD538547 - Sequence 519571 from Patent EP1572962.
JD160152 - Sequence 141176 from Patent EP1572962.
JD126402 - Sequence 107426 from Patent EP1572962.
JD546819 - Sequence 527843 from Patent EP1572962.
JD164556 - Sequence 145580 from Patent EP1572962.
JD473488 - Sequence 454512 from Patent EP1572962.
JD106617 - Sequence 87641 from Patent EP1572962.
JD477762 - Sequence 458786 from Patent EP1572962.
JD536569 - Sequence 517593 from Patent EP1572962.
MA580171 - JP 2018138019-A/152097: Polycomb-Associated Non-Coding RNAs.
MA580170 - JP 2018138019-A/152096: Polycomb-Associated Non-Coding RNAs.
MA580168 - JP 2018138019-A/152094: Polycomb-Associated Non-Coding RNAs.
MA580167 - JP 2018138019-A/152093: Polycomb-Associated Non-Coding RNAs.
MA580166 - JP 2018138019-A/152092: Polycomb-Associated Non-Coding RNAs.
MA580165 - JP 2018138019-A/152091: Polycomb-Associated Non-Coding RNAs.
MA580164 - JP 2018138019-A/152090: Polycomb-Associated Non-Coding RNAs.
MA448342 - JP 2018138019-A/20268: Polycomb-Associated Non-Coding RNAs.
MA446779 - JP 2018138019-A/18705: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_mapkPathway - MAPKinase Signaling Pathway

Reactome (by CSHL, EBI, and GO)

Protein O75676 (Reactome details) participates in the following event(s):

R-HSA-374696 Phosphorylation of L1 by p90rsk
R-HSA-437239 Recycling pathway of L1
R-HSA-373760 L1CAM interactions
R-HSA-422475 Axon guidance
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: A8K7Z8, ENST00000334205.1, ENST00000334205.2, ENST00000334205.3, ENST00000334205.4, ENST00000334205.5, ENST00000334205.6, ENST00000334205.7, ENST00000334205.8, KS6A4_HUMAN, MSK2, NM_003942, O75585, O75676, Q53ES8, uc317twp.1, uc317twp.2
UCSC ID: ENST00000334205.9_9
RefSeq Accession: NM_003942.3
Protein: O75676 (aka KS6A4_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.