Human Gene CSNK2A1 (uc002wdx.1) Description and Page Index
  Description: Homo sapiens casein kinase 2, alpha 1 polypeptide (CSNK2A1), transcript variant 2, mRNA.
RefSeq Summary (NM_001895): Casein kinase II is a serine/threonine protein kinase that phosphorylates acidic proteins such as casein. It is involved in various cellular processes, including cell cycle control, apoptosis, and circadian rhythm. The kinase exists as a tetramer and is composed of an alpha, an alpha-prime, and two beta subunits. The alpha subunits contain the catalytic activity while the beta subunits undergo autophosphorylation. The protein encoded by this gene represents the alpha subunit. Multiple transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Apr 2018].
Transcript (Including UTRs)
   Position: hg19 chr20:463,338-524,482 Size: 61,145 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr20:464,605-489,195 Size: 24,591 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr20:463,338-524,482)mRNA (may differ from genome)Protein (391 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Casein kinase II subunit alpha; Short=CK II alpha; EC=;
FUNCTION: Catalytic subunit of a constitutively active serine/threonine-protein kinase complex that phosphorylates a large number of substrates containing acidic residues C-terminal to the phosphorylated serine or threonine. Regulates numerous cellular processes, such as cell cycle progression, apoptosis and transcription, as well as viral infection. May act as a regulatory node which integrates and coordinates numerous signals leading to an appropriate cellular response. During mitosis, functions as a component of the p53/TP53-dependent spindle assembly checkpoint (SAC) that maintains cyclin-B-CDK1 activity and G2 arrest in response to spindle damage. Also required for p53/TP53-mediated apoptosis, phosphorylating 'Ser-392' of p53/TP53 following UV irradiation. Can also negatively regulate apoptosis. Phosphorylates the caspases CASP9 and CASP2 and the apoptotic regulator NOL3. Phosphorylation protects CASP9 from cleavage and activation by CASP8, and inhibits the dimerization of CASP2 and activation of CASP8. Regulates transcription by direct phosphorylation of RNA polymerases I, II, III and IV. Also phosphorylates and regulates numerous transcription factors including NF-kappa-B, STAT1, CREB1, IRF1, IRF2, ATF1, SRF, MAX, JUN, FOS, MYC and MYB. Phosphorylates Hsp90 and its co-chaperones FKBP4 and CDC37, which is essential for chaperone function. Regulates Wnt signaling by phosphorylating CTNNB1 and the transcription factor LEF1. Acts as an ectokinase that phosphorylates several extracellular proteins. During viral infection, phosphorylates various proteins involved in the viral life cycles of EBV, HSV, HBV, HCV, HIV, CMV and HPV.
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
ENZYME REGULATION: Constitutively active protein kinase whose activity is not directly affected by phosphorylation. Seems to be regulated by level of expression and localization.
SUBUNIT: Heterotetramer composed of two catalytic subunits (alpha chain and/or alpha' chain) and two regulatory subunits (beta chains). The tetramer can exist as a combination of 2 alpha/2 beta, 2 alpha'/2 beta or 1 alpha/1 alpha'/2 beta subunits. Also part of a CK2-SPT16-SSRP1 complex composed of SSRP1, SUPT16H, CSNK2A1, CSNK2A2 and CSNK2B, which forms following UV irradiation. Interacts with RNPS1.
INTERACTION: O00257-3:CBX4; NbExp=2; IntAct=EBI-347804, EBI-4392727; P19784:CSNK2A2; NbExp=2; IntAct=EBI-347804, EBI-347451; P67870:CSNK2B; NbExp=10; IntAct=EBI-347804, EBI-348169; O60282:KIF5C; NbExp=4; IntAct=EBI-347804, EBI-717170; P29590:PML; NbExp=2; IntAct=EBI-347804, EBI-295890; Q96EB6:SIRT1; NbExp=2; IntAct=EBI-347804, EBI-1802965;
PTM: Phosphorylated at Thr-344, Thr-360, Ser-362 and Ser-370 by CDK1 in prophase and metaphase and dephosphorylated during anaphase. Phosphorylation does not directly affect casein kinase 2 activity, but may contribute to its regulation by forming binding sites for interacting proteins and/or targeting it to different compartments.
MISCELLANEOUS: Can use both ATP and GTP as phosphoryl donors. Phosphorylation by casein kinase 2 has been estimated to represent up to one quarter of the eukaryotic phosphoproteome. Casein kinase 2 has been found to be inccreased at protein level and up- regulated at the level of enzyme activity in the majority of cancers. However, elevated levels of casein kinase 2 are present in certain normal organs such as brain and testes.
SIMILARITY: Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. CK2 subfamily.
SIMILARITY: Contains 1 protein kinase domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CSNK2A1
CDC HuGE Published Literature: CSNK2A1

-  MalaCards Disease Associations
  MalaCards Gene Search: CSNK2A1
Diseases sorted by gene-association score: okur-chung neurodevelopmental syndrome* (1230), pachygyria (6), cardiomyopathy, dilated, 1p (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D010634 Phenobarbital
  • C029790 2,2',3',4,4',5-hexachlorobiphenyl
  • C014211 2,3,7,8-tetrachlorodibenzofuran
  • C023514 2,6-dinitrotoluene
  • C492322 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole
  • C023035 3,4,5,3',4'-pentachlorobiphenyl
  • C009505 4,4'-diaminodiphenylmethane
  • C405354 4,5,6,7-tetrabromobenzotriazole
  • C012606 4-vinyl-1-cyclohexene dioxide
  • D000082 Acetaminophen
          more ... click here to view the complete list

+  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: 28.92 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 695.00 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 -101.50276-0.368 Picture PostScript Text
3' UTR -375.301267-0.296 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
IPR011009 - Kinase-like_dom
IPR000719 - Prot_kinase_cat_dom
IPR017441 - Protein_kinase_ATP_BS
IPR002290 - Ser/Thr_dual-sp_kinase_dom
IPR008271 - Ser/Thr_kinase_AS

Pfam Domains:
PF00069 - Protein kinase domain
PF01636 - Phosphotransferase enzyme family
PF07714 - Protein tyrosine kinase

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

Protein Data Bank (PDB) 3-D Structure
MuPIT help

- X-ray MuPIT

- X-ray MuPIT

- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2PVR - X-ray MuPIT 2ZJW - X-ray MuPIT 3AMY - X-ray MuPIT
3AT2 - X-ray MuPIT 3AT3 - X-ray MuPIT 3AT4 - X-ray MuPIT
3AXW - X-ray MuPIT 3BQC - X-ray MuPIT 3C13 - X-ray MuPIT
3FWQ - X-ray MuPIT 3H30 - X-ray MuPIT 3JUH - X-ray MuPIT
3MB6 - X-ray MuPIT 3MB7 - X-ray MuPIT 3NGA - X-ray MuPIT
3NSZ - X-ray MuPIT 3OWJ - X-ray MuPIT 3OWK - X-ray MuPIT
3OWL - X-ray MuPIT 3PE1 - X-ray MuPIT 3PE2 - X-ray MuPIT
3PE4 - X-ray MuPIT 3Q04 - X-ray MuPIT 3Q9W - X-ray MuPIT
3Q9X - X-ray MuPIT 3Q9Y - X-ray MuPIT 3Q9Z - X-ray MuPIT
3QA0 - X-ray MuPIT 3R0T - X-ray MuPIT 3RPS - X-ray MuPIT
3TAX - X-ray MuPIT 3U4U - X-ray MuPIT 3U87 - X-ray MuPIT
3U9C - X-ray MuPIT 4DGL - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P68400
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0042802 identical protein binding
GO:0047485 protein N-terminus binding
GO:0051879 Hsp90 protein binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006468 protein phosphorylation
GO:0006915 apoptotic process
GO:0007049 cell cycle
GO:0007165 signal transduction
GO:0008284 positive regulation of cell proliferation
GO:0016055 Wnt signaling pathway
GO:0016310 phosphorylation
GO:0018107 peptidyl-threonine phosphorylation
GO:0030177 positive regulation of Wnt signaling pathway
GO:0030307 positive regulation of cell growth
GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0045732 positive regulation of protein catabolic process
GO:0048511 rhythmic process
GO:0061077 chaperone-mediated protein folding
GO:1901796 regulation of signal transduction by p53 class mediator

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005956 protein kinase CK2 complex
GO:0016580 Sin3 complex
GO:0016581 NuRD complex
GO:0031519 PcG protein complex

-  Descriptions from all associated GenBank mRNAs
  DQ354583 - Homo sapiens casein kinase 2 alpha isoform mRNA, complete cds.
BC050036 - Homo sapiens casein kinase 2, alpha 1 polypeptide, mRNA (cDNA clone MGC:51015 IMAGE:5298655), complete cds.
M55265 - Human casein kinase II alpha subunit mRNA, complete cds.
J02853 - Homo sapiens casein kinase II alpha subunit mRNA, complete cds.
S53149 - Homo sapiens casein kinase II-alpha subunit mRNA, complete cds.
AK302583 - Homo sapiens cDNA FLJ57289 complete cds, highly similar to Casein kinase II subunit alpha (EC
BC002615 - Homo sapiens cDNA clone IMAGE:3140817, containing frame-shift errors.
BC011668 - Homo sapiens casein kinase 2, alpha 1 polypeptide, mRNA (cDNA clone MGC:15232 IMAGE:4121882), complete cds.
AK312535 - Homo sapiens cDNA, FLJ92904, highly similar to Homo sapiens casein kinase 2, alpha 1 polypeptide (CSNK2A1), mRNA.
AY735339 - Homo sapiens casein kinase 2 alpha 1 subunit transcript variant 3, 5' UTR.
BC071167 - Homo sapiens casein kinase 2, alpha 1 polypeptide, mRNA (cDNA clone MGC:88038 IMAGE:5772615), complete cds.
BC053532 - Homo sapiens casein kinase 2, alpha 1 polypeptide, mRNA (cDNA clone MGC:61540 IMAGE:3908058), complete cds.
JD072520 - Sequence 53544 from Patent EP1572962.
JD294996 - Sequence 276020 from Patent EP1572962.
JD181980 - Sequence 163004 from Patent EP1572962.
JD204118 - Sequence 185142 from Patent EP1572962.
JD484094 - Sequence 465118 from Patent EP1572962.
JD077153 - Sequence 58177 from Patent EP1572962.
JD314210 - Sequence 295234 from Patent EP1572962.
JD303025 - Sequence 284049 from Patent EP1572962.
JD289986 - Sequence 271010 from Patent EP1572962.
JD154000 - Sequence 135024 from Patent EP1572962.
JD093205 - Sequence 74229 from Patent EP1572962.
JD441988 - Sequence 423012 from Patent EP1572962.
JD105028 - Sequence 86052 from Patent EP1572962.
JD301995 - Sequence 283019 from Patent EP1572962.
JD314652 - Sequence 295676 from Patent EP1572962.
JD073095 - Sequence 54119 from Patent EP1572962.
JD485410 - Sequence 466434 from Patent EP1572962.
JD055631 - Sequence 36655 from Patent EP1572962.
JD544284 - Sequence 525308 from Patent EP1572962.
JD193647 - Sequence 174671 from Patent EP1572962.
AB451279 - Homo sapiens CSNK2A1 mRNA for casein kinase II alpha 1 subunit isoform a, complete cds, clone: FLJ08116AAAN.
BT019792 - Homo sapiens casein kinase 2, alpha 1 polypeptide mRNA, complete cds.
DQ893102 - Synthetic construct clone IMAGE:100005732; FLH193758.01X; RZPDo839B0979D casein kinase 2, alpha 1 polypeptide (CSNK2A1) gene, encodes complete protein.
KJ890987 - Synthetic construct Homo sapiens clone ccsbBroadEn_00381 CSNK2A1 gene, encodes complete protein.
KJ905186 - Synthetic construct Homo sapiens clone ccsbBroadEn_14604 CSNK2A1 gene, encodes complete protein.
DQ896374 - Synthetic construct Homo sapiens clone IMAGE:100010834; FLH193754.01L; RZPDo839B0969D casein kinase 2, alpha 1 polypeptide (CSNK2A1) gene, encodes complete protein.
AB451411 - Homo sapiens CSNK2A1 mRNA for casein kinase II alpha 1 subunit isoform a, partial cds, clone: FLJ08116AAAF.
AB590210 - Synthetic construct DNA, clone: pFN21AB6554, Homo sapiens CSNK2A1 gene for casein kinase 2, alpha 1 polypeptide, without stop codon, in Flexi system.
CU680000 - Synthetic construct Homo sapiens gateway clone IMAGE:100023360 5' read CSNK2A1 mRNA.
DQ595336 - Homo sapiens piRNA piR-61448, complete sequence.
JD528960 - Sequence 509984 from Patent EP1572962.
JD564068 - Sequence 545092 from Patent EP1572962.
JD300545 - Sequence 281569 from Patent EP1572962.
JD492206 - Sequence 473230 from Patent EP1572962.
DQ587598 - Homo sapiens piRNA piR-54710, complete sequence.
JD110918 - Sequence 91942 from Patent EP1572962.
JD094883 - Sequence 75907 from Patent EP1572962.
JD080727 - Sequence 61751 from Patent EP1572962.
JD087961 - Sequence 68985 from Patent EP1572962.
JD495834 - Sequence 476858 from Patent EP1572962.
JD124872 - Sequence 105896 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04310 - Wnt signaling pathway
hsa04520 - Adherens junction
hsa04530 - Tight junction

BioCarta from NCI Cancer Genome Anatomy Project
h_il2Pathway - IL 2 signaling pathway
h_il6Pathway - IL 6 signaling pathway
h_igf1Pathway - IGF-1 Signaling Pathway
h_egfPathway - EGF Signaling Pathway
h_ngfPathway - Nerve growth factor pathway (NGF)
h_TPOPathway - TPO Signaling Pathway
h_wntPathway - WNT Signaling Pathway
h_Lis1Pathway - Lissencephaly gene (LIS1) in neuronal migration and development
h_insulinPathway - Insulin Signaling Pathway
h_epoPathway - EPO Signaling Pathway
h_pdgfPathway - PDGF Signaling Pathway

Reactome (by CSHL, EBI, and GO)

Protein P68400 (Reactome details) participates in the following event(s):

R-HSA-392752 Phosphorylation of L1 by CK-II
R-HSA-6805061 CK2 binds FACT
R-HSA-201717 CSNK2-mediated phosphorylation of DVL
R-HSA-2529020 CK2 phosphorylates condensin I subunits
R-HSA-6814409 CK2 phosphorylates PDCL
R-HSA-8948039 FUNDC1 is phosphorylated by CK2
R-HSA-8850945 Casein kinase II phosphorylates PTEN
R-HSA-8873929 Casein kinase II phosphorylates STARD10
R-HSA-6805059 CK2:FACT phosphorylates TP53
R-HSA-8937989 RUNX1 binds PRC1 complexes
R-HSA-445144 Signal transduction by L1
R-HSA-6804756 Regulation of TP53 Activity through Phosphorylation
R-HSA-373760 L1CAM interactions
R-HSA-201688 WNT mediated activation of DVL
R-HSA-2514853 Condensation of Prometaphase Chromosomes
R-HSA-6814122 Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding
R-HSA-8934903 Receptor Mediated Mitophagy
R-HSA-8948751 Regulation of PTEN stability and activity
R-HSA-1483191 Synthesis of PC
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-422475 Axon guidance
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-68877 Mitotic Prometaphase
R-HSA-390466 Chaperonin-mediated protein folding
R-HSA-5205647 Mitophagy
R-HSA-6807070 PTEN Regulation
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-1266738 Developmental Biology
R-HSA-195721 Signaling by WNT
R-HSA-68886 M Phase
R-HSA-391251 Protein folding
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-1483257 Phospholipid metabolism
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-212436 Generic Transcription Pathway
R-HSA-162582 Signal Transduction
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-392499 Metabolism of proteins
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-556833 Metabolism of lipids
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-1640170 Cell Cycle
R-HSA-1430728 Metabolism
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B4DYS6, CK2A1, CSK21_HUMAN, D3DVV8, NM_001895, NP_808228, P19138, P20426, P68400, Q14013, Q5U065
UCSC ID: uc002wdx.1
RefSeq Accession: NM_001895
Protein: P68400 (aka CSK21_HUMAN or KC21_HUMAN)
CCDS: CCDS13003.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001895.3
exon count: 13CDS single in 3' UTR: no RNA size: 2732
ORF size: 1176CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2552.00frame shift in genome: no % Coverage: 99.52
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.