PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries

Uenishi, Hirohide; Eguchi, Tetsuo; Suzuki, Kohei; Sawazaki, T.; Toki, Daisuke; Shinkai, Hiroki; Okumura, Naohiko; Hamasima, Noriyuki; Awata, Takashi

doi:10.1093/nar/gkh037

Cited by 83 publications

(62 citation statements)

References 21 publications

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“…To further verify the pFcRn-S, the nucleotide sequence of the pFcRn-S (EF208068) was used to search the EST database using Megablast (optimized for highly similar sequences), (www.ncbi.nlm.hig.gov/blast). At least three EST sequences, BP142288.1, EW289930.1, and EW284029.1, were identified [34,35] and the nucleotides spanning α2 and α3 domain were perfectly aligned (Fig.2D). This suggests that the pFcRn-S lacks of α2 domain of the full length counterpart.…”

Section: Splicing Form Of Pfcrn Lacks α2 Domainmentioning

confidence: 91%

Identification and characterization of an alternatively spliced variant of the MHC class I-related porcine neonatal Fc receptor for IgG

Tuo

Liu

et al. 2008

Developmental & Comparative Immunology

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The neonatal Fc receptor for IgG (FcRn) functions to transport maternal IgG to the fetal/neonatal animals and protects IgG from catabolism. The present study identified two pFcRn cDNAs (1.071 kb and 0.795 kb) from intestinal epithelial cells. The corresponding mRNA transcripts were detected in porcine kidney cell line LLC-PK1, peripheral blood mononuclear cells and porcine tissues by RT-PCR and Northern blot. Sequence analysis showed that the 1.071 kb cDNA encodes the full-length pFcRn (pFcRn-L); whereas the 0.795 kb cDNA codes for a truncated pFcRn (pFcRn-S) with deletion of 92 amino acids matching to the alpha2 domain of pFcRn-L. The pFcRn-L was constitutively expressed by epithelial cells; however, pFcRn-S was not detectable in porcine tissues and cell lines although its transcript was abundant. Despite of the lack of native pFcRn-S, pFcRn-S was readily detected in transfected cells. Recombinant pFcRn-L was confirmed to bind IgG at pH 6.0, but not pH 7.5; however, pFcRn-S failed to bind IgG at both pH 5.0-6.0 and 7.5. The pFcRn-L was expressed on the cell surface and mainly localized in early endosomes. In contrast, pFcRn-S was absent from cell surface and primarily localized in the lysosome and pFcRn-S trafficking to lysosomes was independent of β2m. The accumulation of pFcRn-S in the lysosome may explain the absence detection of native pFcRn-S protein expression. In addition, the trafficking of pFcRn-S to the lysosomal compartment suggests that in addition to sorting signals in its cytoplasmic tail, the FcRn structural integrity may be important for proper intracellular trafficking and function.

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Section: Splicing Form Of Pfcrn Lacks α2 Domainmentioning

confidence: 91%

Identification and characterization of an alternatively spliced variant of the MHC class I-related porcine neonatal Fc receptor for IgG

Tuo

Liu

et al. 2008

Developmental & Comparative Immunology

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“…In the case of IFNAR1 , a publicly available porcine cDNA sequence (accession AB116561) was also used for the assembly. The availability of porcine 5 -ESTs from full-length enriched cDNA libraries proved to be essential for this strategy (Uenishi et al, 2004).…”

Section: Assembly Of Cdna Sequencesmentioning

confidence: 99%

Sequence analysis of the porcine <i>IFNAR1</i> and <i>IFNGR2</i> genes

Leeb

Dolle²,

Haase³

2006

Cytogenet Genome Res

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A porcine BAC clone harboring the tightly linked IFNAR1 and IFNGR2 genes was identified by comparative analysis of the publicly available porcine BAC end sequences. The complete 168,835 bp insert sequence of this clone was determined. Sequence comparisons of the genomic sequence with EST sequences from public databases were performed and allowed a detailed annotation of the IFNAR1 and IFNGR2 genes. The analyzed genes showed a conserved genomic organization with their known mammalian orthologs, however the sequence conservation of these genes across species was relatively low. In addition to the IFNAR1 and IFNGR2 genes, which were completely sequenced, the analyzed BAC clone also contained parts of an orphan gene encoding a putative transmembrane protein (TMEM50B). In contrast to the IFNAR1 and IFNGR2 genes the sequence conservation of the TMEM50B gene across different mammalian species was extremely high.

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“…In previous studies (Charo et al, 1994;Yu et al, 2000), human CCR2 and CCR9 were shown to have two isoforms due to alternative splicing; our results derived from RACE analysis (data not shown) implied that the alternative forms of CCR2 and CCR9 (CCR2A and CCR9B, respectively) do not exist in pigs. Sequencing of clones from porcine cDNA libraries enriched for fulllength inserts (Uenishi et al, 2004) revealed a single, long form of CCR9 (the homologue of human CCR9A) and no homologue of CCR9B.…”

Section: Comparative Analysis Of the CC Chemokine Receptor Regions Ofmentioning

confidence: 99%

Genomic structure of eight porcine chemokine receptors and intergene sharing of an exon between CCR1 and XCR1

Shinkai¹,

Morozumi²,

Toki³

et al. 2005

Gene

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PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries

Cited by 83 publications

References 21 publications

Identification and characterization of an alternatively spliced variant of the MHC class I-related porcine neonatal Fc receptor for IgG

Identification and characterization of an alternatively spliced variant of the MHC class I-related porcine neonatal Fc receptor for IgG

Sequence analysis of the porcine <i>IFNAR1</i> and <i>IFNGR2</i> genes

Genomic structure of eight porcine chemokine receptors and intergene sharing of an exon between CCR1 and XCR1

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