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Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

Oduru S, Campbell JL, Karri S, Hendry WJ, Khan SA, Williams SC - BMC Genomics (2003)

Bottom Line: Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes.The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome.The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, USA. oduru.sreedhar@ttuhsc.edu

ABSTRACT

Background: Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes. We have utilized a comparative genomics approach involving the sequencing of randomly selected hamster testis cDNAs to begin to identify genes not previously annotated on the human, mouse, rat and Fugu (pufferfish) genomes.

Results: 735 distinct sequences were analyzed for their relatedness to known sequences in public databases. Eight of these sequences were derived from previously unidentified genes and expression of these genes in testis was confirmed by Northern blotting. The genomic locations of each sequence were mapped in human, mouse, rat and pufferfish, where applicable, and the structure of their cognate genes was derived using computer-based predictions, genomic comparisons and analysis of uncharacterized cDNA sequences from human and macaque.

Conclusion: The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome. The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted. Each gene was expressed primarily in testis, suggesting that they may play roles in the development and/or function of testicular cells.

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Alignment of human, macaque, mouse and rat 13043 sequences. This alignment was anchored on a single cDNA isolated from macaque (AB0770087). This sequence was compared to the human (Hs), mouse (Mm) and rat (Rn) genomic sequences at Ensembl and individual exons were assigned. One additional potential exon was assigned based on similarity between genomic sequences based on PipMaker analysis. The human and mouse sequences listed here match partially with predicted proteins in both human and mouse (ENSP0000306627 and XP_156183, respectively) but conform more to the template predicted by the macaque sequence. The rat sequence was constructed from genomic sequences AABR02142366, AABR02119574, AABR02127843, AABR02117677 and AABR02097473. Predicted transmembrane domains are underlined in red in the human sequence and a potential nucleotide binding domain is underlined in blue. A putative cation channel in the human, mouse and rat proteins is double underlined in the mouse sequence. The region of similarity to the original hamster clone is indicated with a red dotted underline.
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Figure 8: Alignment of human, macaque, mouse and rat 13043 sequences. This alignment was anchored on a single cDNA isolated from macaque (AB0770087). This sequence was compared to the human (Hs), mouse (Mm) and rat (Rn) genomic sequences at Ensembl and individual exons were assigned. One additional potential exon was assigned based on similarity between genomic sequences based on PipMaker analysis. The human and mouse sequences listed here match partially with predicted proteins in both human and mouse (ENSP0000306627 and XP_156183, respectively) but conform more to the template predicted by the macaque sequence. The rat sequence was constructed from genomic sequences AABR02142366, AABR02119574, AABR02127843, AABR02117677 and AABR02097473. Predicted transmembrane domains are underlined in red in the human sequence and a potential nucleotide binding domain is underlined in blue. A putative cation channel in the human, mouse and rat proteins is double underlined in the mouse sequence. The region of similarity to the original hamster clone is indicated with a red dotted underline.

Mentions: This clone encodes an ORF of 56 amino acids that did not display significant similarity to known proteins. Northern blotting revealed a strong signal in testis (figure 1). Genome comparisons revealed matches on human chromosome 3, mouse chromosome 16 and rat chromosome 11 (Table 2). Human, mouse and rat coding sequences were assembled using a macaque cDNA (AB070087) as template (figure 8). Domain mapping identified several conserved transmembrane domains in each protein as well as a putative cyclic nucleotide binding site close to the C-terminus (figure 2). In addition a putative cation channel was identified in the center of the protein. Further analysis will be necessary to determine whether this protein functions as a regulatable cation channel.


Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

Oduru S, Campbell JL, Karri S, Hendry WJ, Khan SA, Williams SC - BMC Genomics (2003)

Alignment of human, macaque, mouse and rat 13043 sequences. This alignment was anchored on a single cDNA isolated from macaque (AB0770087). This sequence was compared to the human (Hs), mouse (Mm) and rat (Rn) genomic sequences at Ensembl and individual exons were assigned. One additional potential exon was assigned based on similarity between genomic sequences based on PipMaker analysis. The human and mouse sequences listed here match partially with predicted proteins in both human and mouse (ENSP0000306627 and XP_156183, respectively) but conform more to the template predicted by the macaque sequence. The rat sequence was constructed from genomic sequences AABR02142366, AABR02119574, AABR02127843, AABR02117677 and AABR02097473. Predicted transmembrane domains are underlined in red in the human sequence and a potential nucleotide binding domain is underlined in blue. A putative cation channel in the human, mouse and rat proteins is double underlined in the mouse sequence. The region of similarity to the original hamster clone is indicated with a red dotted underline.
© Copyright Policy
Related In: Results  -  Collection

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Figure 8: Alignment of human, macaque, mouse and rat 13043 sequences. This alignment was anchored on a single cDNA isolated from macaque (AB0770087). This sequence was compared to the human (Hs), mouse (Mm) and rat (Rn) genomic sequences at Ensembl and individual exons were assigned. One additional potential exon was assigned based on similarity between genomic sequences based on PipMaker analysis. The human and mouse sequences listed here match partially with predicted proteins in both human and mouse (ENSP0000306627 and XP_156183, respectively) but conform more to the template predicted by the macaque sequence. The rat sequence was constructed from genomic sequences AABR02142366, AABR02119574, AABR02127843, AABR02117677 and AABR02097473. Predicted transmembrane domains are underlined in red in the human sequence and a potential nucleotide binding domain is underlined in blue. A putative cation channel in the human, mouse and rat proteins is double underlined in the mouse sequence. The region of similarity to the original hamster clone is indicated with a red dotted underline.
Mentions: This clone encodes an ORF of 56 amino acids that did not display significant similarity to known proteins. Northern blotting revealed a strong signal in testis (figure 1). Genome comparisons revealed matches on human chromosome 3, mouse chromosome 16 and rat chromosome 11 (Table 2). Human, mouse and rat coding sequences were assembled using a macaque cDNA (AB070087) as template (figure 8). Domain mapping identified several conserved transmembrane domains in each protein as well as a putative cyclic nucleotide binding site close to the C-terminus (figure 2). In addition a putative cation channel was identified in the center of the protein. Further analysis will be necessary to determine whether this protein functions as a regulatable cation channel.

Bottom Line: Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes.The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome.The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, USA. oduru.sreedhar@ttuhsc.edu

ABSTRACT

Background: Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes. We have utilized a comparative genomics approach involving the sequencing of randomly selected hamster testis cDNAs to begin to identify genes not previously annotated on the human, mouse, rat and Fugu (pufferfish) genomes.

Results: 735 distinct sequences were analyzed for their relatedness to known sequences in public databases. Eight of these sequences were derived from previously unidentified genes and expression of these genes in testis was confirmed by Northern blotting. The genomic locations of each sequence were mapped in human, mouse, rat and pufferfish, where applicable, and the structure of their cognate genes was derived using computer-based predictions, genomic comparisons and analysis of uncharacterized cDNA sequences from human and macaque.

Conclusion: The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome. The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted. Each gene was expressed primarily in testis, suggesting that they may play roles in the development and/or function of testicular cells.

Show MeSH
Related in: MedlinePlus