Standardized nomenclature for Alu repeats

Batzer, Mark A.; Deininger, Prescott L.; Hellmann-Blumberg, Utha; Jurka, Jerzy; Labuda, Damian; Rubin, Carol M.; Schmid, Carl W.; Ziętkiewicz, Ewa; Zuckerkandl, Emile

doi:10.1007/bf00163204

Cited by 263 publications

(210 citation statements)

References 36 publications

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“…2) which belong to the relatively old J-subfamily of Alus [49,50]. The upstream Alu is truncated at its 3 ′ end by approximately 195 bp and is flanked by 14 bp direct repeats and is oriented in the opposite direction of the complete downstream Alu element.…”

Section: Resultsmentioning

confidence: 99%

The human hexokinase II gene promoter: functional characterization and detection of variants among patients with NIDDM

1997

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Section: Resultsmentioning

confidence: 99%

The human hexokinase II gene promoter: functional characterization and detection of variants among patients with NIDDM

1997

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“…Depending on the presence of this linker or not, we divided seven lemur subfamilies into two Alu consensus sequences: AluL and AluLa. Using the Alu naming convention (Batzer et al 1996), we tentatively identify these seven subfamilies as AluL, AluL5, AluL6, AluL9, AluLa, AluLa7a, and AluLa7b (Supplemental Table S2) based on these diagnostic nucleotide differences from their consensus sequences (Supplemental Figs. S10 and S11).…”

Section: Alu Repeats In Primate Genomesmentioning

confidence: 99%

Comparative analysis of Alu repeats in primate genomes

Liu¹,

Alkan²,

Lu³

et al. 2009

Genome Res.

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Using bacteria artificial chromosome (BAC) end sequences (16.9 Mb) and high-quality alignments of genomic sequences (17.4 Mb), we performed a global assessment of the divergence distributions, phylogenies, and consensus sequences for Alu elements in primates including lemur, marmoset, macaque, baboon, and chimpanzee as compared to human. We found that in lemurs, Alu elements show a broader and more symmetric sequence divergence distribution, suggesting a steady rate of Alu retrotransposition activity among prosimians. In contrast, Alu elements in anthropoids show a skewed distribution shifted toward more ancient elements with continual declining rates in recent Alu activity along the hominoid lineage of evolution. Using an integrated approach combining mutation profile and insertion/deletion analyses, we identified nine novel lineage-specific Alu subfamilies in lemur (seven), marmoset (one), and baboon/macaque (one) containing multiple diagnostic mutations distinct from their human counterparts-Alu J, S, and Y subfamilies, respectively. Among these primates, we show that that the lemur has the lowest density of Alu repeats (55 repeats/Mb), while marmoset has the greatest abundance (188 repeats/Mb). We estimate that ;70% of lemur and 16% of marmoset Alu elements belong to lineage-specific subfamilies. Our analysis has provided an evolutionary framework for further classification and refinement of the Alu repeat phylogeny. The differences in the distribution and rates of Alu activity have played an important role in subtly reshaping the structure of primate genomes. The functional consequences of these changes among the diverse primate lineages over such short periods of evolutionary time are an important area of future investigation.

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“…CHRNA3 therefore displays a genomic structure (eight exons and seven introns) peculiar among the nAChR gene family. Exon 7 of CHRNA3 is spliced out within an antisense Alu repeat which, on the basis of the nucleotides found at diagnostic positions shared by subfamily members, belongs to the Alu-Sp subfamily (Batzer et al 1996). It is interesting to note that an antisense Alu repeat located within CHRNA3 intron 5 was previously demonstrated to be inserted in the CHRNA3 mRNA by alternative splicing, giving rise to exon 5a (Mihovilovic et al 1993).…”

Section: Discussionmentioning

confidence: 99%

Characterization of the genomic structure of the human neuronal nicotinic acetylcholine receptor CHRNA5/A3/B4 gene cluster and identification of novel intragenic polymorphisms

et al. 2001

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Genes coding for the α5, α3, and 4 subunits (CHRNA5, CHRNA3, and CHRNB4) of the neuronal nicotinic acetylcholine receptors (nAChRs) are clustered on chromosome 15q24. Linkage of this chromosomal region to autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), an idiopathic partial epilepsy, was reported in one family. Moreover, mutations in other neuronal nAChR subunit genes coding for the α4 (CHRNA4) and the 2 (CHRNB2) subunits were associated with ADNFLE. Apart from the exon-intron structure of CHRNA3, the genomic organization of this gene cluster was unknown, making comprehensive mutational analyses impossible. The genomic structure of CHRNA5 and CHRNB4 is here reported. Moreover, two hitherto unknown introns were identified within the 3Ј untranslated region of CHRNA3, causing a partial tail-to-tail overlap with CHRNA5. Four novel intragenic polymorphisms were identified and characterized in the cluster.

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Standardized nomenclature for Alu repeats

Cited by 263 publications

References 36 publications

The human hexokinase II gene promoter: functional characterization and detection of variants among patients with NIDDM

The human hexokinase II gene promoter: functional characterization and detection of variants among patients with NIDDM

Comparative analysis of Alu repeats in primate genomes

Characterization of the genomic structure of the human neuronal nicotinic acetylcholine receptor CHRNA5/A3/B4 gene cluster and identification of novel intragenic polymorphisms

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