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    Cdkal1 CDK5 regulatory subunit associated protein 1-like 1 [ Mus musculus (house mouse) ]

    Gene ID: 68916, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Cdkal1provided by MGI
    Official Full Name
    CDK5 regulatory subunit associated protein 1-like 1provided by MGI
    Primary source
    MGI:MGI:1921765
    See related
    Ensembl:ENSMUSG00000006191 AllianceGenome:MGI:1921765
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    1190005B03Rik; 6620401C13Rik
    Summary
    Enables N6-threonylcarbomyladenosine methylthiotransferase activity. Acts upstream of or within maintenance of translational fidelity and tRNA methylthiolation. Located in rough endoplasmic reticulum. Is expressed in olfactory epithelium and testis. Used to study type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in diabetes mellitus; gestational diabetes; and type 2 diabetes mellitus. Orthologous to human CDKAL1 (CDK5 regulatory subunit associated protein 1 like 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis adult (RPKM 1.1), bladder adult (RPKM 0.6) and 25 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Cdkal1 in Genome Data Viewer
    Location:
    13 A3.1- A3.2; 13 12.93 cM
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (29375729..30039665, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (29191746..29855683, complement)

    Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA A330102I10 gene Neighboring gene STARR-seq mESC enhancer starr_34046 Neighboring gene predicted gene, 53781 Neighboring gene STARR-seq mESC enhancer starr_34047 Neighboring gene STARR-seq mESC enhancer starr_34048 Neighboring gene STARR-seq mESC enhancer starr_34049 Neighboring gene STARR-seq mESC enhancer starr_34050 Neighboring gene STARR-positive B cell enhancer ABC_E8521 Neighboring gene STARR-seq mESC enhancer starr_34055 Neighboring gene STARR-seq mESC enhancer starr_34056 Neighboring gene STARR-positive B cell enhancer mm9_chr13:29830009-29830310 Neighboring gene CapStarr-seq enhancer MGSCv37_chr13:29838382-29838565 Neighboring gene STARR-positive B cell enhancer ABC_E7218 Neighboring gene CapStarr-seq enhancer MGSCv37_chr13:29947409-29947592 Neighboring gene predicted gene, 52084 Neighboring gene STARR-positive B cell enhancer ABC_E9871 Neighboring gene STARR-positive B cell enhancer ABC_E211 Neighboring gene STARR-seq mESC enhancer starr_34059 Neighboring gene E2F transcription factor 3 Neighboring gene predicted gene, 40860

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Cdkal1, a type 2 diabetes susceptibility gene, regulates mitochondrial function in adipose tissue. Palmer CJ, et al. Mol Metab, 2017 Oct. PMID 29031721, Free PMC Article
    2. CDK5 Regulatory Subunit-Associated Protein 1-like 1 Negatively Regulates Adipocyte Differentiation through Activation of Wnt Signaling Pathway. Take K, et al. Sci Rep, 2017 Aug 4. PMID 28779110, Free PMC Article
    3. Hepatic Cdkal1 deletion regulates HDL catabolism and promotes reverse cholesterol transport. An DB, et al. Atherosclerosis, 2023 Jun. PMID 37245423
    4. Irp2 regulates insulin production through iron-mediated Cdkal1-catalyzed tRNA modification. Santos MCFD, et al. Nat Commun, 2020 Jan 15. PMID 31941883, Free PMC Article
    5. Deletion of CDKAL1 affects high-fat diet-induced fat accumulation and glucose-stimulated insulin secretion in mice, indicating relevance to diabetes. Okamura T, et al. PLoS One, 2012. PMID 23173044, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Hepatic Cdkal1 deletion regulates HDL catabolism and promotes reverse cholesterol transport.
      Title: Hepatic Cdkal1 deletion regulates HDL catabolism and promotes reverse cholesterol transport.
    2. Cdkal1 catalyzes methylthiolation of t6A37 in tRNALysUUU to ms2t6A37.
      Title: Irp2 regulates insulin production through iron-mediated Cdkal1-catalyzed tRNA modification.
    3. Our results identify CDKAL1 as novel negative regulator of adipocyte differentiation and provide insights into the link between CDKAL1 and metabolic diseases such as type 2 diabetes and obesity.
      Title: CDK5 Regulatory Subunit-Associated Protein 1-like 1 Negatively Regulates Adipocyte Differentiation through Activation of Wnt Signaling Pathway.
    4. Cdkal1 is necessary for normal mitochondrial morphology and function in adipose tissue. These results suggest that the type 2 diabetes susceptibility gene CDKAL1 has novel functions in regulating mitochondrial activity.
      Title: Cdkal1, a type 2 diabetes susceptibility gene, regulates mitochondrial function in adipose tissue.
    5. CDKAL1 may affect such compensatory mechanisms regulating glucose homeostasis through interaction with diet
      Title: Deletion of CDKAL1 affects high-fat diet-induced fat accumulation and glucose-stimulated insulin secretion in mice, indicating relevance to diabetes.
    6. Knockout mice with pancreatic beta-cell-specific lack of cdkal1 show pancreatic islet hypertrophy and impaired blood glucose control.
      Title: Functional loss of Cdkal1, a novel tRNA modification enzyme, causes the development of type 2 diabetes.
    7. Data show that Cdkal1 is a mammalian methylthiotransferase that biosynthesizes 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A) in tRNA(Lys)(UUU) and that it is required for the accurate translation of AAA and AAG codons.
      Title: Deficit of tRNA(Lys) modification by Cdkal1 causes the development of type 2 diabetes in mice.
    8. CDKAL1 controls first-phase insulin exocytosis in beta cells by facilitating ATP generation, K(ATP) channel responsiveness and the subsequent activity of Ca(2+) channels through pathways other than CDK5-mediated regulation
      Title: Deletion of CDKAL1 affects mitochondrial ATP generation and first-phase insulin exocytosis.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables 4 iron, 4 sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables N6-threonylcarbomyladenosine methylthiotransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables N6-threonylcarbomyladenosine methylthiotransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables catalytic activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables iron-sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methylthiotransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables tRNA (N(6)-L-threonylcarbamoyladenosine(37)-C(2))-methylthiotransferase IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within maintenance of translational fidelity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tRNA methylthiolation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within tRNA methylthiolation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tRNA modification IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within tRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in rough endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    threonylcarbamoyladenosine tRNA methylthiotransferase
    Names
    tRNA-t(6)A37 methylthiotransferase
    NP_001295415.1
    NP_653119.1
    XP_006516825.1
    XP_006516826.1
    XP_006516827.1
    XP_011242644.1
    XP_017171078.1
    XP_017171079.1
    XP_036014044.1
    XP_036014045.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001308486.2 → NP_001295415.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform 2

      See identical proteins and their annotated locations for NP_001295415.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks multiple alternate 3' exons and contains two alternate 3' exons, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL513025
      Consensus CDS
      CCDS84016.1
      UniProtKB/Swiss-Prot
      Q91WE6
      Related
      ENSMUSP00000089262.6, ENSMUST00000091674.12
      Conserved Domains (1) summary
      pfam00919
      Location:64 → 94
      UPF0004; Uncharacterized protein family UPF0004

    2. NM_144536.4 → NP_653119.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform 1

      See identical proteins and their annotated locations for NP_653119.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AL512647, AL513025, AL589701, AL645587
      Consensus CDS
      CCDS26412.1
      UniProtKB/Swiss-Prot
      Q3TE97, Q3V3D2, Q5T0I5, Q8C4B0, Q91WE6, Q9CT69
      Related
      ENSMUSP00000006353.8, ENSMUST00000006353.14
      Conserved Domains (3) summary
      cd01335
      Location:207 → 410
      Radical_SAM; Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. ...
      TIGR01578
      Location:64 → 491
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type
      pfam00919
      Location:64 → 145
      UPF0004; Uncharacterized protein family UPF0004

    RNA

    1. NR_131896.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate 3' exon and contains two alternate 3' exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL512647, AL513025, AL589701, AL645587, AL645746
      Related
      ENSMUST00000140278.8

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000079.7 Reference GRCm39 C57BL/6J

      Range
      29375729..30039665 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017315589.3 → XP_017171078.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4

      Conserved Domains (1) summary
      TIGR01578
      Location:1 → 206
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type

    2. XM_036158151.1 → XP_036014044.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X1

      Conserved Domains (1) summary
      TIGR01578
      Location:44 → 440
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type

    3. XM_006516763.5 → XP_006516826.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4

      See identical proteins and their annotated locations for XP_006516826.1

      Conserved Domains (1) summary
      TIGR01578
      Location:1 → 206
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type

    4. XM_006516762.5 → XP_006516825.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X3

      Conserved Domains (1) summary
      TIGR01578
      Location:8 → 253
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type

    5. XM_036158152.1 → XP_036014045.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4

      Conserved Domains (1) summary
      TIGR01578
      Location:1 → 206
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type

    6. XM_017315590.3 → XP_017171079.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4

      Conserved Domains (1) summary
      TIGR01578
      Location:1 → 206
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type

    7. XM_006516764.5 → XP_006516827.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4

      See identical proteins and their annotated locations for XP_006516827.1

      Conserved Domains (1) summary
      TIGR01578
      Location:1 → 206
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type

    8. XM_011244342.4 → XP_011242644.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X2

      Conserved Domains (1) summary
      TIGR01578
      Location:64 → 422
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q91WE6.1 GenPept UniProtKB/Swiss-Prot:Q91WE6

    Gene LinkOut

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