Database for chicken full-length cDNAs

The generation of full-length cDNA databases is essential for functional genomics studies as well as for correct annotation of species genomic sequences. Human and mouse full-length cDNA projects have provided the biomedical research community with a large amount of gene information. Recent completion of the chicken genome sequence draft now enables a similar full-length cDNA project to be initiated for this species. In this report, we introduce the development of a chicken full-length cDNA database, which will facilitate future research work in this biological system. In this project, chicken expressed sequence tags (ESTs) were aligned onto human and mouse full-length cDNAs (or open reading frames) on the basis of their similarity. More than 588,000 chicken ESTs were aligned to ∼170,000 full-length human and mouse templates obtained from the NEDO, RIKEN, and MGC databases. Many of these templates have known biological functions, and their orthologous chicken genes in the EMBL database are also provided in our database, which is available at http://bioinfo.hku.hk/chicken/ . We will continue to collect known chicken full-length cDNAs to update the database for public use. The cDNA alignment results presented herein and on our database will be useful for animal science and veterinary researchers wishing to clone and to confirm full-length chicken cDNAs of interest.

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Generation and Analysis of Expressed Sequence Tags (ESTs) from Muscle Full-Length cDNA Library of Wujin Pig

Journal of Integrative Agriculture ◽

10.1016/s2095-3119(13)60414-1 ◽

2014 ◽

Vol 13 (2) ◽

pp. 378-386

Author(s):

Su-mei ZHAO ◽

Yong-gang LIU ◽

Hong-bing PAN ◽

Xi ZHANG ◽

Chang-rong GE ◽

...

Keyword(s):

Cdna Library ◽

Expressed Sequence Tags ◽

Full Length ◽

Full Length Cdna ◽

Expressed Sequence

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Beta-centractin: characterization and distribution of a new member of the centractin family of actin-related proteins.

Molecular Biology of the Cell ◽

10.1091/mbc.5.12.1301 ◽

1994 ◽

Vol 5 (12) ◽

pp. 1301-1310 ◽

Cited By ~ 28

Author(s):

S W Clark ◽

O Staub ◽

I B Clark ◽

E L Holzbaur ◽

B M Paschal ◽

...

Keyword(s):

Amino Acid ◽

Cdna Clone ◽

Expressed Sequence Tag ◽

Full Length ◽

Northern Analysis ◽

Related Protein ◽

Two Dimensional Gel Electrophoresis ◽

Full Length Cdna ◽

Dynactin Complex ◽

Expressed Sequence

An examination of human-expressed sequence tags indicated the existence of an isoform of centractin, an actin-related protein localized to microtubule-associated structures. Using one of these tags, we isolated and determined the nucleotide sequence of a full-length cDNA clone. The protein encoded represents the first example of multiple isoforms of an actin-related protein in a single organism. Northern analysis using centractin-specific probes revealed three species of mRNA in HeLa cells that could encode centractin isoforms. One mRNA encodes the previously-identified centractin (now referred to as alpha-centractin). The full-length cDNA clone isolated using the expressed sequence tag encodes a new member of the centractin family, beta-centractin. A probe specific for alpha-centractin hybridized to the third species of mRNA observed (referred to as gamma-centractin). Comparisons of Northern blots of human tissues indicated that alpha-centractin and beta-centractin mRNAs are equally distributed in all populations of mRNA examined, whereas the expression of gamma-centractin appears to be tissue specific. The amino acid sequence of beta-centractin, deduced from the cDNA, indicates a 91% identity with alpha-centractin, increasing to 96% similarity when conservative amino acid changes are taken into account. As antibodies previously raised against alpha-centractin reacted only poorly with beta-centractin, new antibodies were produced and combined with two-dimensional gel electrophoresis to discriminate the two isoforms. Using this system, the subcellular distribution of the alpha- and beta-isoforms were determined. Both isoforms were found predominantly in the cytosolic fraction as a part of a previously identified 20S complex (referred to as the dynactin complex) with no evidence for a free pool of either isoform. The isoforms were found in a constant ratio of approximately 15:1 (alpha:beta) in the dynactin complex.

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Generation and comparative analysis of full-length transcriptomes in sweetpotato and its putative wild ancestor I. trifida

10.1101/112425 ◽

2017 ◽

Cited By ~ 6

Author(s):

Yonghai Luo ◽

Na Ding ◽

Xuan Shi ◽

Yunxiang Wu ◽

Ruyuan Wang ◽

...

Keyword(s):

Comparative Analysis ◽

Ipomoea Batatas ◽

Large Scale ◽

Full Length ◽

Open Reading Frames ◽

High Quality ◽

Evolutionary Pattern ◽

Full Length Cdna ◽

Cdna Sequences ◽

Public Datasets

AbstractSweetpotato [Ipomoea batatas (L.) Lam.] is one of the most important crops in many developing countries and provides a candidate source of bioenergy. However, neither high-quality reference genome nor large-scale full-length cDNA sequences for this outcrossing hexaploid are still lacking, which in turn impedes progress in research studies in sweetpotato functional genomics and molecular breeding. In this study, we apply a combination of second- and third-generation sequencing technologies to sequence full-length transcriptomes in sweetpotato and its putative ancestor I. trifida. In total, we obtained 53,861/51,184 high-quality transcripts, which includes 34,963/33,637 putative full-length cDNA sequences, from sweetpotato/I. trifida. Amongst, we identified 104,540/94,174 open reading frames, 1476/1475 transcription factors, 25,315/27,090 simple sequence repeats, 417/531 long non-coding RNAs out of the sweetpotato/I. trifida dataset. By utilizing public available genomic contigs, we analyzed the gene features (including exon number, exon size, intron number, intron size, exon-intron structure) of 33,119 and 32,793 full-length transcripts in sweetpotato and I. trifida, respectively. Furthermore, comparative analysis between our transcript datasets and other large-scale cDNA datasets from different plant species enables us assessing the quality of public datasets, estimating the genetic similarity across relative species, and surveyed the evolutionary pattern of genes. Overall, our study provided fundamental resources of large-scale full-length transcripts in sweetpotato and its putative ancestor, for the first time, and would facilitate structural, functional and comparative genomics studies in this important crop.

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