TITLE

In silico identification and expression of SLC30 family genes: An expressed sequence tag data mining strategy for the characterization of zinc transporters' tissue expression

AUTHOR(S)
Seve, Michel; Chimienti, Fabrice; Devergnas, Séverine; Favier, Alain
PUB. DATE
January 2004
SOURCE
BMC Genomics;2004, Vol. 5, p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Intracellular zinc concentration and localization are strictly regulated by two main protein components, metallothioneins and membrane transporters. In mammalian cells, two membrane transporters family are involved in intracellular zinc homeostasis: the uptake transporters called SLC39 or Zip family and the efflux transporters called SLC30 or ZnT family. ZnT proteins are members of the cation diffusion facilitator (CDF) family of metal ion transporters. Results: From genomic databanks analysis, we identified the full-length sequences of two novel SLC30 genes, SLC30A8 and SLC30A10, extending the SLC30 family to ten members. We used an expressed sequence tag (EST) data mining strategy to determine the pattern of ZnT genes expression in tissues. In silico results obtained for already studied ZnT sequences were compared to experimental data, previously published. We determined an overall good correlation with expression pattern obtained by RT-PCR or immunomethods, particularly for highly tissue specific genes. Conclusion: The method presented herein provides a useful tool to complete gene families from sequencing programs and to produce preliminary expression data to select the proper biological samples for laboratory experimentation.
ACCESSION #
28859322

 

Related Articles

  • SAGE is far more sensitive than EST for detecting low-abundance transcripts. Miao Sun; Guolin Zhou; Sanggyu Lee; Jianjun Chen; Run Zhang Shi; San Ming Wang // BMC Genomics;2004, Vol. 5, p1 

    Background: Isolation of low-abundance transcripts expressed in a genome remains a serious challenge in transcriptome studies. The sensitivity of the methods used for analysis has a direct impact on the efficiency of the detection. We compared the EST method and the SAGE method to determine...

  • Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation. Armstead, Ian; Lin Huang; King, Julie; Ougham, Helen; Thomas, Howard; King, Ian // BMC Genomics;2007, Vol. 8, p283 

    Background: Various methods have been developed to explore inter-genomic relationships among plant species. Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding...

  • A new species of the genus Tigriopus (Copepoda: Harpacticoida: Harpacticidae) from Antarctica. Park, Eun-Ok; Lee, Seunghan; Cho, Mijin; Yoon, Suk Hyun; Lee, Yoon; Lee, Wonchoel // Proceedings of the Biological Society of Washington;Jul2014, Vol. 127 Issue 1, p138 

    Tigriopus kingsejongensis, new species, is described from tidal pools near the King Sejong Station on King George Island, Antarctica. The new species is closely related to Tigriopus kerguelenensis from Kerguelen Island. Both species share several characters, including the presence of an...

  • Isolation and Characterization of an AGAMOUS Homologue PmAG from the Japanese Apricot ( Prunus mume Sieb. et Zucc.). Hou, Ji-Hua; Gao, Zhi-Hong; Zhang, Zhen; Chen, Su-Mei; Ando, Toshi; Zhang, Ji-Yu; Wang, Xin-Wei // Plant Molecular Biology Reporter;Jun2011, Vol. 29 Issue 2, p473 

    n AGAMOUS homologue, named PmAG (GenBank accession number EU068730), was isolated from the Japanese apricot cultivar 'Shirokaga' ( Prunus mume) via the homology cloning method. The cDNA was 812-base pairs long with an open reading frame of 732 base pairs, and encoded for a putative protein of...

  • Whole Genome Duplication and Enrichment of Metal Cation Transporters Revealed by De Novo Genome Sequencing of Extremely Halotolerant Black Yeast Hortaea werneckii. Lenassi, Metka; Gostinčar, Cene; Jackman, Shaun; Turk, Martina; Sadowski, Ivan; Nislow, Corey; Jones, Steven; Birol, Inanc; Cimerman, Nina Gunde; Plemenitaš, Ana // PLoS ONE;Aug2013, Vol. 8 Issue 8, p1 

    Hortaea werneckii, ascomycetous yeast from the order Capnodiales, shows an exceptional adaptability to osmotically stressful conditions. To investigate this unusual phenotype we obtained a draft genomic sequence of a H. werneckii strain isolated from hypersaline water of solar saltern. Two of...

  • ZifBASE: a database of zinc finger proteins and associated resources. Jayakanthan, Mannu; Muthukumaran, Jayaraman; Chandrasekar, Sanniyasi; Chawla, Konika; Punetha, Ankita; Sundar, Durai // BMC Genomics;2009, Vol. 10, p421 

    Background: Information on the occurrence of zinc finger protein motifs in genomes is crucial to the developing field of molecular genome engineering. The knowledge of their target DNA-binding sequences is vital to develop chimeric proteins for targeted genome engineering and site-specific gene...

  • Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues. Zaghlool, Ammar; Ameur, Adam; Nyberg, Linnea; Halvardson, Jonatan; Grabherr, Manfred; Cavelier, Lucia; Feuk, Lars // BMC Biotechnology;2013, Vol. 13 Issue 1, p1 

    Background The starting material for RNA sequencing (RNA-seq) studies is usually total RNA or polyA+RNA. Both forms of RNA represent heterogeneous pools of RNA molecules at different levels of maturation and processing. Such heterogeneity, in addition to the biases associated with...

  • Analysis and Comparison of Partial Sequences of Clones from a Taste-bud-enriched cDNA Library. Hoon, M. A.; Ryba, N. J. P. // Journal of Dental Research;Apr1997, Vol. 76 Issue 4, p831 

    Differential patterns of cellular development and function are determined, at least in part, by the specific gene expression of particular cells. Thus, determination of differential patterns of gene expression between tissues is likely to help elucidate molecular details of tissue-specific...

  • The PrP-like protein Doppel gene in sheep and cattle: cDNA sequence and expression. Tranulis, Michael A.; Espenes, Arild; Comincini, Sergio; Skretting, Grethe; Harbitz, Ingrid // Mammalian Genome;May2001, Vol. 12 Issue 5, p376 

    cDNAs encoding the ovine and bovine prion protein-like protein Doppel (Dpl) have been cloned. Sequencing revealed cDNAs of 2.85 and 3.31 kb from ovine and bovine testicular tissue, in accordance with observations of single transcripts of 3.2 and 3.6 kb on Northern blots. Sequence alignments...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics