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

Gene ID: 54901, updated on 8-Jul-2021

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
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
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Genomic context

See CDKAL1 in Genome Data Viewer
Location:
6p22.3
Exon count:
22
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (20534457..21232404)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (20534688..21232635)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene E2F3 intronic transcript 1 Neighboring gene RNA, U6 small nuclear 141, pseudogene Neighboring gene E2F transcription factor 3 Neighboring gene uncharacterized LOC105374968 Neighboring gene uncharacterized LOC107986577 Neighboring gene ribosomal protein L36a pseudogene 25 Neighboring gene VISTA enhancer hs1340 Neighboring gene Sharpr-MPRA regulatory region 659 Neighboring gene RNA, U6 small nuclear 150, pseudogene Neighboring gene uncharacterized LOC105374966 Neighboring gene uncharacterized LOC107986578 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
  • 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

Associated conditions

Description Tests
A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans.
GeneReviews: Not available
A genome-wide association study of gestational diabetes mellitus in Korean women.
GeneReviews: Not available
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.
GeneReviews: Not available
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.
GeneReviews: Not available
A variant in CDKAL1 influences insulin response and risk of type 2 diabetes.
GeneReviews: Not available
Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.
GeneReviews: Not available
Association of glycosylated hemoglobin with the gene encoding CDKAL1 in the Korean Association Resource (KARE) study.
GeneReviews: Not available
Common variants at CDKAL1 and KLF9 are associated with body mass index in east Asian populations.
GeneReviews: Not available
Confirmation of multiple risk Loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population.
GeneReviews: Not available
Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia.
GeneReviews: Not available
Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.
GeneReviews: Not available
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
GeneReviews: Not available
Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
GeneReviews: Not available
Genome-wide association study identifies multiple loci associated with bladder cancer risk.
GeneReviews: Not available
Genome-wide association study identifies three novel loci for type 2 diabetes.
GeneReviews: Not available
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
GeneReviews: Not available
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
GeneReviews: Not available
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
GeneReviews: Not available
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
GeneReviews: Not available
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
GeneReviews: Not available
Meta-analysis identifies common variants associated with body mass index in east Asians.
GeneReviews: Not available
Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
GeneReviews: Not available
Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index.
GeneReviews: Not available
Multiple nonglycemic genomic loci are newly associated with blood level of glycated hemoglobin in East Asians.
GeneReviews: Not available
New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism.
GeneReviews: Not available
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.
GeneReviews: Not available
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
GeneReviews: Not available
Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.
GeneReviews: Not available
SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations.
GeneReviews: Not available
Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases.
GeneReviews: Not available
Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia.
GeneReviews: Not available
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
GeneReviews: Not available

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

Homology

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
PubMed 
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
PubMed 
Component Evidence Code Pubs
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
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_016866476.1
XP_024302249.1

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.

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
    Q5VV42
    Related
    ENSP00000274695.4, ENST00000274695.8
    Conserved Domains (1) summary
    cl27627
    Location:65445
    UPF0004; Uncharacterized protein family UPF0004

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. 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
  2. XM_024446481.1XP_024302249.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X1

    Conserved Domains (1) summary
    cl27627
    Location:65445
    UPF0004; Uncharacterized protein family UPF0004
  3. XM_017010986.1XP_016866475.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4

    Conserved Domains (1) summary
    TIGR01578
    Location:65423
    MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type
  4. XM_011514719.2XP_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
  5. XM_017010987.1XP_016866476.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X5

RNA

  1. XR_001743500.1 RNA Sequence

  2. XR_001743501.1 RNA Sequence

  3. XR_926266.2 RNA Sequence

  4. XR_926265.2 RNA Sequence

  5. XR_926267.2 RNA Sequence

  6. XR_001743495.2 RNA Sequence

  7. XR_001743496.2 RNA Sequence

  8. XR_001743498.2 RNA Sequence

  9. XR_001743499.2 RNA Sequence

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