Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences

Abstract

The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene. ESTs were generated from libraries enriched for full-length cDNAs and analyzed to identify candidate full-ORF clones, which then were sequenced to high accuracy. The MGC has currently sequenced and verified the full ORF for a nonredundant set of >9,000 human and >6,000 mouse genes. Candidate full-ORF clones for an additional 7,800 human and 3,500 mouse genes also have been identified. All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:͞͞mgc.nci.nih.gov).T he gene content of the mammalian genome is a topic of great interest. While draft sequences are now available for the human (1, 2), mouse (www.ensembl.org͞Mus musculus), and rat (http:͞͞hgsc.bcm.tmc.edu͞projects͞rat) genomes, the challenge remains to correctly identify all of the encoded genes. Difficulty in deciphering the anatomy of mammalian genes is due to several factors, including large amounts of intervening (noncoding) sequence, the imperfection of gene-prediction algorithms (3), and the incompleteness of cDNA-sequence resources, many of which consist of gene tags of variable length and quality. Full-length cDNA sequences are extremely useful for determining the genomic structure of genes, especially when analyzed within the context of genomic sequence. To facilitate geneidentification efforts and to catalyze experimental investigation, the National Institutes of Health (NIH) launched the Mammalian Gene Collection (MGC) program (4) with the aim of providing freely accessible, high-quality sequences for validated, complete ORF cDNA clones. In this article, we describe our progress toward the goal of identifying and accurately sequencing at least one full ORF-containing cDNA clone for each human and mouse gene, as well as making these fully sequenced clones available without restriction. Materials and MethodscDNA Library Production. MGC cDNA libraries were prepared from a diverse set of tissues and cell lines, in several different vector systems, by using a variety of methods. Vector maps and details of library construction are available at http:͞͞mgc. nci.nih.gov͞Info͞VectorMaps. The complete sequences for each of the MGC vectors can be found at http:͞͞image.llnl.gov͞ image͞html͞vectors.shtml. The catalog of MGC cDNA libraries can be accessed at http:͞͞mgc.nci.nih.gov.

Identification of SERINC5-001 as the Predominant Spliced Isoform for HIV-1 Restriction

“…Full-length human cDNA clones have been isolated previously for Ser5-001, -004, -005, -008a, and -008b (22)(23)(24)(25). One other isoform that could encode a protein is Ser5-201 ( Fig.…”

Comparison of Caspase Genes for the Induction of Apoptosis Following Gene Delivery

“…The primer sequences used for the detection of murine granzyme B (Locus: BC002085, Accession: BC002085) [36] were as follows:…”

A Molecular Analysis of the Na+-Independent Cation Chloride Cotransporters

“…, AK294059, AK295096, and AK098371) suggest that hKCC2b pre-mRNAs maybe subjected to additional splicing events. In Figure 4A, there are four full-length hKCC2 cDNAs: AF208159 [32], BC132668, BC132670 [33] and AK289758. In silico analysis also revealed three hKCC2b transcripts: hKCC2b-s1 (AK294059) created by exclusion of exons 4-9, hKCC2b-s2 (AK295096) created by exclusion of exons 3-20, and hKCC2b-s3 (AK098371) created by the inclusion of an alternative stop codon located in exon 8.…”

“…Interestingly, two other transcripts i.e. , BC033894 [33] and AK292550, which also encode hKCC3a proteins, differ in their 5'- and 3'-UTRs relative to AF105366 and AF116242. This peculiarity of different transcripts encoding the same protein may reflect potential translational regulatory properties.…”