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Aliases for CDKAL1 Gene

Aliases for CDKAL1 Gene

  • CDK5 Regulatory Subunit Associated Protein 1 Like 1 2 3 5
  • TRNA-T(6)A37 Methylthiotransferase 3 4
  • Threonylcarbamoyladenosine TRNA Methylthiotransferase 3
  • CDK5 Regulatory Subunit-Associated Protein 1-Like 1 4
  • CDK5 Regulatory Subunit Associated Protein 1-Like 1 2
  • EC 4

External Ids for CDKAL1 Gene

Previous GeneCards Identifiers for CDKAL1 Gene

  • GC06P020597
  • GC06P020642
  • GC06P020478

Summaries for CDKAL1 Gene

Entrez Gene Summary for CDKAL1 Gene

  • The protein encoded by this gene is a member of the methylthiotransferase family. The function of this gene is not known. Genome-wide association studies have linked single nucleotide polymorphisms in an intron of this gene with susceptibilty to type 2 diabetes. [provided by RefSeq, May 2010]

GeneCards Summary for CDKAL1 Gene

CDKAL1 (CDK5 Regulatory Subunit Associated Protein 1 Like 1) is a Protein Coding gene. Diseases associated with CDKAL1 include Diabetes Mellitus, Noninsulin-Dependent and Sapho Syndrome. Among its related pathways are tRNA processing and Gene Expression. Gene Ontology (GO) annotations related to this gene include transferase activity and iron-sulfur cluster binding. An important paralog of this gene is CDK5RAP1.

UniProtKB/Swiss-Prot for CDKAL1 Gene

  • Catalyzes the methylthiolation of N6-threonylcarbamoyladenosine (t(6)A), leading to the formation of 2-methylthio-N6-threonylcarbamoyladenosine (ms(2)t(6)A) at position 37 in tRNAs that read codons beginning with adenine.

Additional gene information for CDKAL1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDKAL1 Gene

Genomics for CDKAL1 Gene

GeneHancer (GH) Regulatory Elements for CDKAL1 Gene

Promoters and enhancers for CDKAL1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J020400 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 715.6 -131.1 -131096 6 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 CDKAL1 E2F3 E2F3-IT1 ENSG00000233848 KRT18P38 UQCRFS1P3 MBOAT1 RN7SL128P
GH06J020533 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 674.6 +0.3 297 2.1 HDGF PKNOX1 SMAD1 FOXA2 ARID4B SIN3A DMAP1 IRF4 YY1 SLC30A9 CDKAL1 LOC105374968
GH06J020200 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 37.4 -327.2 -327227 13.5 HDGF PKNOX1 ARNT SIN3A ZNF2 IRF4 YY1 ZNF766 CBX5 ZNF143 MBOAT1 E2F3 CDKAL1 E2F3-IT1 UQCRFS1P3 KRT18P38 ENSG00000233848 LOC105374961 LOC101928573 LOC105374965
GH06J019802 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE 20.4 -729.9 -729853 3.3 PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF213 LOC100506885 ENSG00000228412 CDKAL1 ID4 GC06M019684 GC06M019417 GC06M019801
GH06J020875 Enhancer 1.5 FANTOM5 Ensembl ENCODE 18.4 +343.3 343262 4.6 FOXA2 SMAD1 MLX ARID4B SIN3A ZNF2 IRF4 YY1 SLC30A9 FOS CDKAL1 GC06P020868 GC06M020943
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDKAL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CDKAL1 gene promoter:
  • Egr-1
  • Pax-4a
  • FOXO3b
  • FOXO3a
  • FOXO3
  • Ik-1
  • STAT1
  • STAT1alpha
  • STAT1beta
  • Gfi-1

Genomic Locations for CDKAL1 Gene

Genomic Locations for CDKAL1 Gene
697,948 bases
Plus strand
697,948 bases
Plus strand

Genomic View for CDKAL1 Gene

Genes around CDKAL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDKAL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDKAL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDKAL1 Gene

Proteins for CDKAL1 Gene

  • Protein details for CDKAL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Threonylcarbamoyladenosine tRNA methylthiotransferase
    Protein Accession:
    Secondary Accessions:
    • A8K6S0
    • Q6P385
    • Q6ZR27
    • Q9NXB3

    Protein attributes for CDKAL1 Gene

    579 amino acids
    Molecular mass:
    65111 Da
    Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
    Quaternary structure:
    No Data Available
    • Sequence=BAC87494.1; Type=Frameshift; Positions=575; Evidence={ECO:0000305};

    Alternative splice isoforms for CDKAL1 Gene


neXtProt entry for CDKAL1 Gene

Post-translational modifications for CDKAL1 Gene

  • Ubiquitination at posLast=516516, posLast=334334, Lys243, Lys172, posLast=150150, Lys112, and Lys45
  • Modification sites at PhosphoSitePlus

Other Protein References for CDKAL1 Gene

No data available for DME Specific Peptides for CDKAL1 Gene

Domains & Families for CDKAL1 Gene

Gene Families for CDKAL1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for CDKAL1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the methylthiotransferase family. CDKAL1 subfamily.
  • Belongs to the methylthiotransferase family. CDKAL1 subfamily.
genes like me logo Genes that share domains with CDKAL1: view

Function for CDKAL1 Gene

Molecular function for CDKAL1 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the methylthiolation of N6-threonylcarbamoyladenosine (t(6)A), leading to the formation of 2-methylthio-N6-threonylcarbamoyladenosine (ms(2)t(6)A) at position 37 in tRNAs that read codons beginning with adenine.
UniProtKB/Swiss-Prot CatalyticActivity:
N(6)-L-threonylcarbamoyladenine(37) in tRNA + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced electron acceptor = 2-methylthio-N(6)-L-threonylcarbamoyladenine(37) in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5-deoxyadenosine + electron acceptor.

Enzyme Numbers (IUBMB) for CDKAL1 Gene

Phenotypes From GWAS Catalog for CDKAL1 Gene

Gene Ontology (GO) - Molecular Function for CDKAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003824 catalytic activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0016740 transferase activity IEA --
GO:0035596 methylthiotransferase activity IBA --
genes like me logo Genes that share ontologies with CDKAL1: view
genes like me logo Genes that share phenotypes with CDKAL1: view

Animal Models for CDKAL1 Gene

MGI Knock Outs for CDKAL1:
  • Cdkal1 Cdkal1<tm2b(EUCOMM)Wtsi>
  • Cdkal1 Cdkal1<tm2a(EUCOMM)Wtsi>
  • Cdkal1 Cdkal1<tm1.2Tomik>

Animal Model Products

miRNA for CDKAL1 Gene

miRTarBase miRNAs that target CDKAL1

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CDKAL1 Gene

Localization for CDKAL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDKAL1 Gene

Endoplasmic reticulum membrane; Single-pass membrane protein. Note=Is a tail-anchored protein that exploits the TCR40 pathway for insertion into the endoplasmic reticulum.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CDKAL1 gene
Compartment Confidence
endoplasmic reticulum 4
cytosol 2
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CDKAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IBA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005791 rough endoplasmic reticulum IEA --
GO:0016020 membrane IEA,HDA 19946888
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CDKAL1: view

Pathways & Interactions for CDKAL1 Gene

genes like me logo Genes that share pathways with CDKAL1: view

Pathways by source for CDKAL1 Gene

Gene Ontology (GO) - Biological Process for CDKAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006400 tRNA modification TAS --
GO:0008033 tRNA processing IEA --
GO:0008150 biological_process ND --
GO:0035600 tRNA methylthiolation IEA --
GO:1990145 maintenance of translational fidelity IEA --
genes like me logo Genes that share ontologies with CDKAL1: view

No data available for SIGNOR curated interactions for CDKAL1 Gene

Drugs & Compounds for CDKAL1 Gene

(2) Drugs for CDKAL1 Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Dipeptidyl peptidase 4 (DPP-4) inhibitors Pharma 0
Tumor necrosis factor alpha (TNF-alpha) inhibitors Pharma 0

(1) Additional Compounds for CDKAL1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
genes like me logo Genes that share compounds with CDKAL1: view

Transcripts for CDKAL1 Gene

Unigene Clusters for CDKAL1 Gene

CDK5 regulatory subunit associated protein 1-like 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDKAL1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
SP1: -
SP2: -
SP3: - -

Relevant External Links for CDKAL1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CDKAL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDKAL1 Gene

Protein differential expression in normal tissues from HIPED for CDKAL1 Gene

This gene is overexpressed in Breast (40.0) and Bone (22.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CDKAL1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CDKAL1 Gene:


SOURCE GeneReport for Unigene cluster for CDKAL1 Gene:


mRNA Expression by UniProt/SwissProt for CDKAL1 Gene:

Tissue specificity: Expressed in pancreatic islets.

Evidence on tissue expression from TISSUES for CDKAL1 Gene

  • Pancreas(2.6)
genes like me logo Genes that share expression patterns with CDKAL1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDKAL1 Gene

Orthologs for CDKAL1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CDKAL1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CDKAL1 34 33
  • 99.87 (n)
(Canis familiaris)
Mammalia CDKAL1 34 33
  • 90.37 (n)
(Bos Taurus)
Mammalia CDKAL1 34 33
  • 90.25 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 88 (a)
-- 34
  • 84 (a)
(Mus musculus)
Mammalia Cdkal1 16 34 33
  • 86.52 (n)
(Ornithorhynchus anatinus)
Mammalia CDKAL1 34
  • 85 (a)
(Gallus gallus)
Aves CDKAL1 34 33
  • 82.46 (n)
(Anolis carolinensis)
Reptilia CDKAL1 34
  • 87 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cdkal1 33
  • 78.95 (n)
MGC76088 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.13079 33
(Danio rerio)
Actinopterygii cdkal1 34 33
  • 69.15 (n)
zgc65864 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005211 33
  • 58.75 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6550 34 33
  • 58.49 (n)
(Caenorhabditis elegans)
Secernentea Y92H12BL.1 34 33
  • 57.41 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G72090 33
  • 57.56 (n)
(Oryza sativa)
Liliopsida Os04g0434300 33
  • 55.49 (n)
Os.11755 33
(Zea mays)
Liliopsida Zm.5072 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5502 34
  • 59 (a)
Species where no ortholog for CDKAL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CDKAL1 Gene

Gene Tree for CDKAL1 (if available)
Gene Tree for CDKAL1 (if available)
Evolutionary constrained regions (ECRs) for CDKAL1: view image

Paralogs for CDKAL1 Gene

Paralogs for CDKAL1 Gene

genes like me logo Genes that share paralogs with CDKAL1: view

Variants for CDKAL1 Gene

Sequence variations from dbSNP and Humsavar for CDKAL1 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs10946398 uncertain-significance, Diabetes mellitus type 2 20,660,803(+) A/C genic_upstream_transcript_variant, intron_variant
rs7756992 uncertain-significance, Diabetes mellitus type 2 20,679,478(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000002750 -- 20,743,625(+) G/A/T genic_upstream_transcript_variant, intron_variant
rs1000003030 -- 21,088,652(+) A/C intron_variant
rs1000004245 -- 20,885,782(+) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CDKAL1 Gene

Variant ID Type Subtype PubMed ID
esv1117045 CNV insertion 17803354
esv2034903 CNV deletion 18987734
esv2356880 CNV deletion 18987734
esv2532671 CNV deletion 19546169
esv2533735 CNV deletion 19546169
esv2658301 CNV deletion 23128226
esv2672282 CNV deletion 23128226
esv2731673 CNV deletion 23290073
esv2731674 CNV deletion 23290073
esv2731675 CNV deletion 23290073
esv2731676 CNV deletion 23290073
esv2763539 CNV loss 21179565
esv3448415 CNV insertion 20981092
esv3567386 CNV deletion 23714750
esv3567388 CNV deletion 23714750
esv3567389 CNV deletion 23714750
esv3570793 CNV loss 25503493
esv3608297 CNV loss 21293372
esv3608299 CNV gain 21293372
esv3608300 CNV gain 21293372
esv3608301 CNV loss 21293372
esv3608302 CNV gain 21293372
esv3608305 CNV loss 21293372
esv3608306 CNV loss 21293372
esv3608307 CNV loss 21293372
esv3890796 CNV loss 25118596
esv5216 CNV loss 18987735
esv9437 CNV loss 19470904
nsv1018397 CNV gain 25217958
nsv1024963 CNV gain 25217958
nsv1026540 CNV loss 25217958
nsv1027005 CNV loss 25217958
nsv1030344 CNV loss 25217958
nsv1074384 CNV deletion 25765185
nsv1117607 CNV deletion 24896259
nsv1124043 CNV deletion 24896259
nsv1137068 CNV deletion 24896259
nsv1153188 CNV deletion 26484159
nsv1161342 CNV deletion 26073780
nsv348939 CNV deletion 16902084
nsv476683 CNV novel sequence insertion 20440878
nsv478636 CNV novel sequence insertion 20440878
nsv478806 CNV novel sequence insertion 20440878
nsv510018 OTHER sequence alteration 20534489
nsv519141 CNV loss 19592680
nsv521200 CNV loss 19592680
nsv524280 CNV loss 19592680
nsv524793 CNV loss 19592680
nsv527696 CNV loss 19592680
nsv528152 CNV gain 19592680
nsv830600 CNV loss 17160897
nsv950137 CNV duplication 24416366
nsv956929 CNV deletion 24416366

Variation tolerance for CDKAL1 Gene

Residual Variation Intolerance Score: 30.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.14; 69.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDKAL1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDKAL1 Gene

Disorders for CDKAL1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CDKAL1 Gene - From: LncRNADisease, HGMD, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
diabetes mellitus, noninsulin-dependent
  • niddm
sapho syndrome
  • synovitis, acne, pustulosis palmaris, hyperostosis, osteomyelitis syndrome
diabetes mellitus
  • diabetes
- elite association - COSMIC cancer census association via MalaCards


  • Diabetes mellitus, non-insulin-dependent (NIDDM) [MIM:125853]: A multifactorial disorder of glucose homeostasis caused by a lack of sensitivity to the bodys own insulin. Affected individuals usually have an obese body habitus and manifestations of a metabolic syndrome characterized by diabetes, insulin resistance, hypertension and hypertriglyceridemia. The disease results in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269 PubMed:17460697, ECO:0000269 PubMed:17463246}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Additional Disease Information for CDKAL1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CDKAL1: view

No data available for Genatlas for CDKAL1 Gene

Publications for CDKAL1 Gene

  1. A variant in CDKAL1 influences insulin response and risk of type 2 diabetes. (PMID: 17460697) Steinthorsdottir V … Stefansson K (Nature genetics 2007) 3 4 44 58
  2. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. (PMID: 17463246) Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research … Purcell S (Science (New York, N.Y.) 2007) 3 4 44 58
  3. Variations in the HHEX gene are associated with increased risk of type 2 diabetes in the Japanese population. (PMID: 17928989) Horikoshi M … Kadowaki T (Diabetologia 2007) 3 22 44 58
  4. CDK5 regulatory subunit-associated protein 1-like 1 (CDKAL1) is a tail-anchored protein in the endoplasmic reticulum (ER) of insulinoma cells. (PMID: 23048041) Brambillasca S … Solimena M (The Journal of biological chemistry 2012) 3 4 58
  5. Common variants at CDKAL1 and KLF9 are associated with body mass index in east Asian populations. (PMID: 22344221) Okada Y … Tanaka T (Nature genetics 2012) 3 44 58

Products for CDKAL1 Gene

Sources for CDKAL1 Gene

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