U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    CDKAL1 CDK5 regulatory subunit associated protein 1 like 1 [ Homo sapiens (human) ]

    Gene ID: 54901, updated on 3-Nov-2024

    Summary

    Official Symbol
    CDKAL1provided by HGNC
    Official Full Name
    CDK5 regulatory subunit associated protein 1 like 1provided by HGNC
    Primary source
    HGNC:HGNC:21050
    See related
    Ensembl:ENSG00000145996 MIM:611259; AllianceGenome:HGNC:21050
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    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]
    Expression
    Ubiquitous expression in thyroid (RPKM 1.8), endometrium (RPKM 1.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CDKAL1 in Genome Data Viewer
    Location:
    6p22.3
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (20534457..21232404)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (20406474..21104535)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (20534688..21232635)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:20467153-20467794 Neighboring gene E2F3 intronic transcript 1 Neighboring gene RNA, U6 small nuclear 141, pseudogene Neighboring gene E2F transcription factor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24130 Neighboring gene uncharacterized LOC124901273 Neighboring gene MPRA-validated peak5719 silencer Neighboring gene uncharacterized LOC105374968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:20629440-20630213 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:20630214-20630986 Neighboring gene NANOG hESC enhancer GRCh37_chr6:20686272-20686773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16981 Neighboring gene MPRA-validated peak5720 silencer Neighboring gene ribosomal protein L36a pseudogene 25 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:20798064-20798254 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:20810592-20811186 Neighboring gene MPRA-validated peak5721 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr6:20834311-20834850 Neighboring gene VISTA enhancer hs1340 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:20877312-20878511 Neighboring gene Sharpr-MPRA regulatory region 659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24134 Neighboring gene MPRA-validated peak5723 silencer Neighboring gene RNA, U6 small nuclear 150, pseudogene Neighboring gene uncharacterized LOC105374966 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:21150224 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:21163919 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 6:21164131 and 6:21164145 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:21166705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24135 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:21186041-21186767 Neighboring gene NANOG hESC enhancer GRCh37_chr6:21223372-21223889 Neighboring gene uncharacterized LOC107986578 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:21230452-21231651 Neighboring gene Sharpr-MPRA regulatory region 5810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:21263602-21264102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:21275814-21276318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:21276319-21276823 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21327213-21328056 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21361231-21362046 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:21362047-21362861 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21367138-21367689 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21367690-21368242 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21368243-21368793 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21393485-21394340 Neighboring gene MPRA-validated peak5728 silencer Neighboring gene uncharacterized LOC107986579 Neighboring gene long intergenic non-protein coding RNA 581

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans.
    EBI GWAS Catalog
    A genome-wide association study of gestational diabetes mellitus in Korean women.
    EBI GWAS Catalog
    A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.
    EBI GWAS Catalog
    A pilot genome-wide association study shows genomic variants enriched in the non-tumor cells of patients with well-differentiated neuroendocrine tumors of the ileum.
    EBI GWAS Catalog
    A variant in CDKAL1 influences insulin response and risk of type 2 diabetes.
    EBI GWAS Catalog
    Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.
    EBI GWAS Catalog
    Association of glycosylated hemoglobin with the gene encoding CDKAL1 in the Korean Association Resource (KARE) study.
    EBI GWAS Catalog
    Common variants at CDKAL1 and KLF9 are associated with body mass index in east Asian populations.
    EBI GWAS Catalog
    Confirmation of multiple risk Loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population.
    EBI GWAS Catalog
    Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia.
    EBI GWAS Catalog
    Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.
    EBI GWAS Catalog
    Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
    EBI GWAS Catalog
    Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci associated with bladder cancer risk.
    EBI GWAS Catalog
    Genome-wide association study identifies three novel loci for type 2 diabetes.
    EBI GWAS Catalog
    Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Meta-analysis identifies common variants associated with body mass index in east Asians.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index.
    EBI GWAS Catalog
    Multiple nonglycemic genomic loci are newly associated with blood level of glycated hemoglobin in East Asians.
    EBI GWAS Catalog
    New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism.
    EBI GWAS Catalog
    New susceptibility loci in MYL2, C12orf51 and OAS1 associated with 1-h plasma glucose as predisposing risk factors for type 2 diabetes in the Korean population.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.
    EBI GWAS Catalog
    SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations.
    EBI GWAS Catalog
    Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases.
    EBI GWAS Catalog
    Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia.
    EBI GWAS Catalog
    Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Messenger RNAs for three proteins AATK, SLC27A1, and CDKAL1 are preferentially secreted out in exosomes from HIV-1 Nef-expressing cells, and their targeting miRNAs (miR-32 and miR-93*) are retained in these cells PubMed
    Vif vif HIV-1 Vif interacts with CDKAL1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ20342, FLJ46705, MGC75469

    Gene Ontology Provided by GOA

    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables tRNA (N(6)-L-threonylcarbamoyladenosine(37)-C(2))-methylthiotransferase IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
     
    involved_in maintenance of translational fidelity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in tRNA methylthiolation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in membrane HDA PubMed 
    located_in rough endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    threonylcarbamoyladenosine tRNA methylthiotransferase
    Names
    tRNA-t(6)A37 methylthiotransferase
    NP_060244.2
    XP_011513020.1
    XP_011513021.1
    XP_016866475.1
    XP_024302249.1
    XP_047274903.1
    XP_047274904.1
    XP_047274905.1
    XP_047274906.1
    XP_047274907.1
    XP_047274908.1
    XP_047274909.1
    XP_047274910.1
    XP_047274911.1
    XP_047274912.1
    XP_047274913.1
    XP_047274914.1
    XP_054211725.1
    XP_054211726.1
    XP_054211727.1
    XP_054211728.1
    XP_054211729.1
    XP_054211730.1
    XP_054211731.1
    XP_054211732.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_021195.2 RefSeqGene

      Range
      5001..702948
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_017774.3NP_060244.2  threonylcarbamoyladenosine tRNA methylthiotransferase

      See identical proteins and their annotated locations for NP_060244.2

      Status: REVIEWED

      Source sequence(s)
      AK128546, AL451080, BC121020
      Consensus CDS
      CCDS4546.1
      UniProtKB/Swiss-Prot
      A8K6S0, Q5VV42, Q6P385, Q6ZR27, Q9NXB3
      Related
      ENSP00000274695.4, ENST00000274695.8
      Conserved Domains (1) summary
      cl27627
      Location:65445
      UPF0004; Uncharacterized protein family UPF0004

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      20534457..21232404
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418949.1XP_047274905.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X1

      UniProtKB/Swiss-Prot
      A8K6S0, Q5VV42, Q6P385, Q6ZR27, Q9NXB3
    2. XM_047418952.1XP_047274908.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X2

    3. XM_011514718.1XP_011513020.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X2

      Conserved Domains (3) summary
      cd01335
      Location:208416
      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:65481
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type
      pfam00919
      Location:65146
      UPF0004; Uncharacterized protein family UPF0004
    4. XM_047418947.1XP_047274903.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X8

    5. XM_047418948.1XP_047274904.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X8

    6. XM_024446481.2XP_024302249.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X8

      Conserved Domains (1) summary
      cl27627
      Location:65445
      UPF0004; Uncharacterized protein family UPF0004
    7. XM_047418950.1XP_047274906.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X9

    8. XM_017010986.2XP_016866475.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4

      Conserved Domains (1) summary
      TIGR01578
      Location:65423
      MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type
    9. XM_011514719.3XP_011513021.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X3

      Conserved Domains (3) summary
      cd01335
      Location:208406
      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. ...
      smart00729
      Location:207420
      Elp3; Elongator protein 3, MiaB family, Radical SAM
      pfam00919
      Location:65146
      UPF0004; Uncharacterized protein family UPF0004
    10. XM_047418958.1XP_047274914.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X7

    11. XM_047418951.1XP_047274907.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X9

    12. XM_047418954.1XP_047274910.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X5

    13. XM_047418955.1XP_047274911.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X6

    14. XM_047418953.1XP_047274909.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X10

    15. XM_047418956.1XP_047274912.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X11

    16. XM_047418957.1XP_047274913.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X11

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      20406474..21104535
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355750.1XP_054211725.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X1

      UniProtKB/Swiss-Prot
      A8K6S0, Q5VV42, Q6P385, Q6ZR27, Q9NXB3
    2. XM_054355752.1XP_054211727.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X2

    3. XM_054355751.1XP_054211726.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X2

    4. XM_054355754.1XP_054211729.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4

    5. XM_054355753.1XP_054211728.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X3

    6. XM_054355757.1XP_054211732.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X7

    7. XM_054355756.1XP_054211731.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X6

    8. XM_054355755.1XP_054211730.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X5

    RNA

    1. XR_008487355.1 RNA Sequence

    2. XR_008487356.1 RNA Sequence

    3. XR_008487354.1 RNA Sequence

    4. XR_008487357.1 RNA Sequence

    5. XR_008487358.1 RNA Sequence

    6. XR_008487359.1 RNA Sequence

    7. XR_008487360.1 RNA Sequence