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

Gene ID: 54901, updated on 12-Aug-2018

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; Vega:OTTHUMG00000014340
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

Genomic context

See CDKAL1 in Genome Data Viewer
Location:
6p22.3
Exon count:
22
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (20534457..21232404)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (20534688..21232635)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 128, pseudogene 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 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Diabetes mellitus type 2
MedGen: C0011860 OMIM: 125853 GeneReviews: Not available
not available

NHGRI GWAS Catalog

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

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • tRNA modification in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    tRNA modification in the nucleus and cytosol, organism-specific biosystemAt least 92 distinct tRNA nucleotide base modifications have been found. The modifications are made post-transcriptionally by a large group of disparate enzymes located in the nucleus, cytosol, and m...
  • tRNA processing, organism-specific biosystem (from REACTOME)
    tRNA processing, organism-specific biosystemGenes encoding transfer RNAs (tRNAs) are transcribed by RNA polymerase III in the nucleus and by mitochondrial RNA polymerase in the mitochondrion.In the nucleus transcription reactions produce precu...

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
4 iron, 4 sulfur cluster binding IEA
Inferred from Electronic Annotation
more info
 
N6-threonylcarbomyladenosine methylthiotransferase activity EXP
Inferred from Experiment
more info
PubMed 
N6-threonylcarbomyladenosine methylthiotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
molecular_function ND
No biological Data available
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
tRNA (N(6)-L-threonylcarbamoyladenosine(37)-C(2))-methylthiotransferase IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
biological_process ND
No biological Data available
more info
 
maintenance of translational fidelity IEA
Inferred from Electronic Annotation
more info
 
tRNA methylthiolation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tRNA methylthiolation IEA
Inferred from Electronic Annotation
more info
 
tRNA modification TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
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)

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_021195.1 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 Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 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

  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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