Human Gene CSNK1A1 (ENST00000377843.8) from GENCODE V44
  Description: Homo sapiens casein kinase 1 alpha 1 (CSNK1A1), transcript variant 2, mRNA. (from RefSeq NM_001892)
Gencode Transcript: ENST00000377843.8
Gencode Gene: ENSG00000113712.19
Transcript (Including UTRs)
   Position: hg38 chr5:149,492,982-149,551,439 Size: 58,458 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg38 chr5:149,496,853-149,550,964 Size: 54,112 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:149,492,982-149,551,439)mRNA (may differ from genome)Protein (337 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: KC1A_HUMAN
DESCRIPTION: RecName: Full=Casein kinase I isoform alpha; Short=CKI-alpha; EC=2.7.11.1; AltName: Full=CK1;
FUNCTION: Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. It can phosphorylate a large number of proteins. Participates in Wnt signaling. Phosphorylates CTNNB1 at 'Ser-45'. May play a role in segregating chromosomes during mitosis.
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
SUBUNIT: Monomer. Interacts with the Axin complex. Interacts with TUT1, leading to TUT1 phosphorylation.
INTERACTION: Q00987:MDM2; NbExp=3; IntAct=EBI-2040168, EBI-389668; Q13546:RIPK1; NbExp=5; IntAct=EBI-1383726, EBI-358507;
SUBCELLULAR LOCATION: Cytoplasm. Cytoplasm, cytoskeleton, centrosome. Chromosome, centromere, kinetochore. Nucleus speckle. Note=Localizes to the centrosome in interphase cells, and to kinetochore fibers during mitosis.
SIMILARITY: Belongs to the protein kinase superfamily. CK1 Ser/Thr protein kinase family. Casein kinase I subfamily.
SIMILARITY: Contains 1 protein kinase domain.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org//Genes/CSNK1A1ID40168ch5q32.html";

-  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           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 45.49 RPKM in Esophagus - Mucosa
Total median expression: 1327.49 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 -201.40475-0.424 Picture PostScript Text
3' UTR -976.903871-0.252 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
IPR008271 - Ser/Thr_kinase_AS

Pfam Domains:
PF00069 - Protein kinase domain

ModBase Predicted Comparative 3D Structure on P48729
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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
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsembl  
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  
AlignmentAlignmentAlignmentAlignment  

-  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

Biological Process:
GO:0000902 cell morphogenesis
GO:0006468 protein phosphorylation
GO:0006909 phagocytosis
GO:0007030 Golgi organization
GO:0007049 cell cycle
GO:0007165 signal transduction
GO:0007166 cell surface receptor signaling pathway
GO:0008360 regulation of cell shape
GO:0016055 Wnt signaling pathway
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0045104 intermediate filament cytoskeleton organization
GO:0051301 cell division
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:1904424 regulation of GTP binding
GO:1904885 beta-catenin destruction complex assembly
GO:1904886 beta-catenin destruction complex disassembly

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000776 kinetochore
GO:0000777 condensed chromosome kinetochore
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0016020 membrane
GO:0016607 nuclear speck
GO:0030877 beta-catenin destruction complex
GO:0036064 ciliary basal body
GO:0042995 cell projection
GO:1990904 ribonucleoprotein complex
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex
GO:0045095 keratin filament


-  Descriptions from all associated GenBank mRNAs
  JD413482 - Sequence 394506 from Patent EP1572962.
JD198177 - Sequence 179201 from Patent EP1572962.
JD337481 - Sequence 318505 from Patent EP1572962.
BC029454 - Homo sapiens cDNA clone IMAGE:4044084.
AF447582 - Homo sapiens HLCDGP1 mRNA, complete cds.
BX647478 - Homo sapiens mRNA; cDNA DKFZp686D05110 (from clone DKFZp686D05110).
BC040473 - Homo sapiens, clone IMAGE:4769127, mRNA.
AF119911 - Homo sapiens PRO2975 mRNA, complete cds.
BC105984 - Homo sapiens cDNA clone IMAGE:3448600.
BC020446 - Homo sapiens cDNA clone IMAGE:3448942.
BC008717 - Homo sapiens casein kinase 1, alpha 1, mRNA (cDNA clone MGC:8504 IMAGE:2822250), complete cds.
BC009186 - Homo sapiens cDNA clone IMAGE:4079854, partial cds.
JD273380 - Sequence 254404 from Patent EP1572962.
AK294099 - Homo sapiens cDNA FLJ51815 complete cds, highly similar to Homo sapiens casein kinase 1, alpha 1 (CSNK1A1), transcript variant 1, mRNA.
JD267264 - Sequence 248288 from Patent EP1572962.
JD086163 - Sequence 67187 from Patent EP1572962.
JD113665 - Sequence 94689 from Patent EP1572962.
AK293761 - Homo sapiens cDNA FLJ55317 complete cds, highly similar to Homo sapiens casein kinase 1, alpha 1 (CSNK1A1), transcript variant 1, mRNA.
JD454872 - Sequence 435896 from Patent EP1572962.
JD332529 - Sequence 313553 from Patent EP1572962.
AK303794 - Homo sapiens cDNA FLJ55318 complete cds, highly similar to Casein kinase I isoform alpha (EC 2.7.11.1).
BX648552 - Homo sapiens mRNA; cDNA DKFZp779B1535 (from clone DKFZp779B1535).
AF218004 - Homo sapiens clone PP2684 unknown mRNA.
JD420614 - Sequence 401638 from Patent EP1572962.
JD425518 - Sequence 406542 from Patent EP1572962.
AK294942 - Homo sapiens cDNA FLJ56335 complete cds, highly similar to Casein kinase I isoform alpha (EC 2.7.11.1).
L37042 - Homo sapiens casein kinase I alpha isoform (CSNK1A1) mRNA, complete cds.
JD469766 - Sequence 450790 from Patent EP1572962.
X80693 - H.sapiens mRNA for protein kinase CK1.
JD552526 - Sequence 533550 from Patent EP1572962.
JD290056 - Sequence 271080 from Patent EP1572962.
JD562353 - Sequence 543377 from Patent EP1572962.
JD205492 - Sequence 186516 from Patent EP1572962.
JD176959 - Sequence 157983 from Patent EP1572962.
JD168723 - Sequence 149747 from Patent EP1572962.
JD091860 - Sequence 72884 from Patent EP1572962.
JD048675 - Sequence 29699 from Patent EP1572962.
JD088276 - Sequence 69300 from Patent EP1572962.
BT019829 - Homo sapiens casein kinase 1, alpha 1 mRNA, complete cds.
BT019830 - Homo sapiens casein kinase 1, alpha 1 mRNA, complete cds.
CR542206 - Homo sapiens full open reading frame cDNA clone RZPDo834H1224D for gene CSNK1A1, casein kinase 1, alpha 1; complete cds, incl. stopcodon.
DQ082865 - Homo sapiens casein kinase 1 alpha 1 (CSNK1A1) mRNA, complete cds, alternatively spliced.
EU668329 - Homo sapiens epididymis secretory sperm binding protein Li 77p (HEL-S-77p) mRNA, partial cds.
KJ896661 - Synthetic construct Homo sapiens clone ccsbBroadEn_06055 CSNK1A1 gene, encodes complete protein.
AB385127 - Synthetic construct DNA, clone: pF1KB5585, Homo sapiens CSNK1A1 gene for casein kinase I isoform alpha, complete cds, without stop codon, in Flexi system.
BC021971 - Homo sapiens casein kinase 1, alpha 1, mRNA (cDNA clone IMAGE:3936929), partial cds.
BC025371 - Homo sapiens casein kinase 1, alpha 1, mRNA (cDNA clone IMAGE:4025440), partial cds.
BC007246 - Homo sapiens casein kinase 1, alpha 1, mRNA (cDNA clone IMAGE:2966714), partial cds.
JD164425 - Sequence 145449 from Patent EP1572962.
JD261436 - Sequence 242460 from Patent EP1572962.
JD190727 - Sequence 171751 from Patent EP1572962.
JD029411 - Sequence 10435 from Patent EP1572962.
JD019652 - Sequence 676 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04310 - Wnt signaling pathway
hsa04340 - Hedgehog signaling pathway

BioCarta from NCI Cancer Genome Anatomy Project
h_nfatPathway - NFAT and Hypertrophy of the heart (Transcription in the broken heart)

Reactome (by CSHL, EBI, and GO)

Protein P48729 (Reactome details) participates in the following event(s):

R-HSA-195251 Assembly of the destruction complex
R-HSA-201685 Beta-catenin is released from the destruction complex
R-HSA-5632671 CSNK1A1 binds SMO dimer
R-HSA-5633040 CSNK1A1 and ADRBK1 dissociate from p-SMO dimer
R-HSA-5229343 AXIN is phosphorylated in the destruction complex
R-HSA-195280 Dissociation of beta-catenin from Axin and association of beta catenin with phospho-(20 aa) APC in the detruction complex
R-HSA-195275 Phosphorylation of APC component of the destruction complex
R-HSA-2130279 Association of beta-catenin with the RBX1:SCF(beta-TrCP1) ubiquitin ligase complex
R-HSA-195304 Association of beta-catenin with the destruction complex
R-HSA-5610718 CK1 phosphorylates p-GLI2
R-HSA-5610722 CK1 phosphorylates p-GLI3
R-HSA-5632670 CSNK1A1 phosphorylates SMO dimer
R-HSA-5632672 ADRBK1 phosphorylates SMO dimer
R-HSA-5632674 ADRBK1 binds phosphorylated SMO dimer
R-HSA-2130286 Multi-ubiquitination of phospho-beta-catenin by RBX1:SCF(beta-TrCP1)
R-HSA-195287 Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3
R-HSA-195318 Phosphorylation of beta-catenin at Ser45 by CK1 alpha
R-HSA-195300 Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3
R-HSA-195283 Phosphorylation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3
R-HSA-195253 Degradation of beta-catenin by the destruction complex
R-HSA-5467337 APC truncation mutants have impaired AXIN binding
R-HSA-5467340 AXIN missense mutants destabilize the destruction complex
R-HSA-5467348 Truncations of AMER1 destabilize the destruction complex
R-HSA-4641262 Disassembly of the destruction complex and recruitment of AXIN to the membrane
R-HSA-5635838 Activation of SMO
R-HSA-195721 Signaling by WNT
R-HSA-4839744 truncated APC mutants destabilize the destruction complex
R-HSA-4839735 AXIN mutants destabilize the destruction complex, activating WNT signaling
R-HSA-4839748 AMER1 mutants destabilize the destruction complex
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-5610783 Degradation of GLI2 by the proteasome
R-HSA-5610785 GLI3 is processed to GLI3R by the proteasome
R-HSA-5632684 Hedgehog 'on' state
R-HSA-5358751 S45 mutants of beta-catenin aren't phosphorylated
R-HSA-5358752 T41 mutants of beta-catenin aren't phosphorylated
R-HSA-5358749 S37 mutants of beta-catenin aren't phosphorylated
R-HSA-5358747 S33 mutants of beta-catenin aren't phosphorylated
R-HSA-196299 Beta-catenin phosphorylation cascade
R-HSA-5339716 Misspliced GSK3beta mutants stabilize beta-catenin
R-HSA-162582 Signal Transduction
R-HSA-4791275 Signaling by WNT in cancer
R-HSA-5610787 Hedgehog 'off' state
R-HSA-5358351 Signaling by Hedgehog
R-HSA-4839743 phosphorylation site mutants of CTNNB1 are not targeted to the proteasome by the destruction complex
R-HSA-5663202 Diseases of signal transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: D3DQG0, D3DQG1, ENST00000377843.1, ENST00000377843.2, ENST00000377843.3, ENST00000377843.4, ENST00000377843.5, ENST00000377843.6, ENST00000377843.7, KC1A_HUMAN, NM_001892, P48729, Q4JJA0, Q5U046, Q5U047, Q6FGA2, Q96HD2, Q9UDK3, uc003lqx.1, uc003lqx.2, uc003lqx.3, uc003lqx.4, uc003lqx.5
UCSC ID: ENST00000377843.8
RefSeq Accession: NM_001892
Protein: P48729 (aka KC1A_HUMAN)
CCDS: CCDS47303.1, CCDS64291.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.