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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 and mouse 15014 sequences. The sequences of human (Hs), mouse (Mm) and macaque (Mf) 15014 orthologues were compared in Align X. The human sequence was derived from XP_089976 (LOC159989). The mouse sequence was obtained from a combination of XP_134746 (LOC234964), a hypothetical protein predicted from the NCBI annotation process along with additional exons predicted from comparisons between the human cDNA and the mouse genomic sequence. The macaque sequence was obtained from Genbank entry BAB63125. Gaps in the human sequence indicate the likely presence of alternative exo ns that may undergo alternative splicing. This hypothesis was supported by exon mapping in both the mouse and rat genome sequences (data not shown). We were unable to detect additional exons in the mouse genomic sequence that might encode the N-terminal sequences in the human protein sequence. The similarity to the hamster clone is underlined.
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Figure 9: Alignment of human, macaque and mouse 15014 sequences. The sequences of human (Hs), mouse (Mm) and macaque (Mf) 15014 orthologues were compared in Align X. The human sequence was derived from XP_089976 (LOC159989). The mouse sequence was obtained from a combination of XP_134746 (LOC234964), a hypothetical protein predicted from the NCBI annotation process along with additional exons predicted from comparisons between the human cDNA and the mouse genomic sequence. The macaque sequence was obtained from Genbank entry BAB63125. Gaps in the human sequence indicate the likely presence of alternative exo ns that may undergo alternative splicing. This hypothesis was supported by exon mapping in both the mouse and rat genome sequences (data not shown). We were unable to detect additional exons in the mouse genomic sequence that might encode the N-terminal sequences in the human protein sequence. The similarity to the hamster clone is underlined.

Mentions: This clone encodes an ORF of 67 amino acids whose mRNA was specifically detected in hamster testis RNA (figure 1). Genome comparisons revealed strong similarities with regions of human chromosome 11, mouse chromosome 9 and rat chromosome 8 (Table 2). This clone matches to hypothetical proteins recently added to the annotation of the human and mouse genomes (FLJ13386 and XP_134746) as well as a protein encoded by a macaque cDNA (BAB63125). The alignment in figure 9 accounts for each of these clones as well as additional exons predicted in the mouse from inter-genome comparisons. The encoded protein contains several predicted coiled-coil regions but no other identifiable functional domains (figure 2).


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 and mouse 15014 sequences. The sequences of human (Hs), mouse (Mm) and macaque (Mf) 15014 orthologues were compared in Align X. The human sequence was derived from XP_089976 (LOC159989). The mouse sequence was obtained from a combination of XP_134746 (LOC234964), a hypothetical protein predicted from the NCBI annotation process along with additional exons predicted from comparisons between the human cDNA and the mouse genomic sequence. The macaque sequence was obtained from Genbank entry BAB63125. Gaps in the human sequence indicate the likely presence of alternative exo ns that may undergo alternative splicing. This hypothesis was supported by exon mapping in both the mouse and rat genome sequences (data not shown). We were unable to detect additional exons in the mouse genomic sequence that might encode the N-terminal sequences in the human protein sequence. The similarity to the hamster clone is underlined.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC161800&req=5

Figure 9: Alignment of human, macaque and mouse 15014 sequences. The sequences of human (Hs), mouse (Mm) and macaque (Mf) 15014 orthologues were compared in Align X. The human sequence was derived from XP_089976 (LOC159989). The mouse sequence was obtained from a combination of XP_134746 (LOC234964), a hypothetical protein predicted from the NCBI annotation process along with additional exons predicted from comparisons between the human cDNA and the mouse genomic sequence. The macaque sequence was obtained from Genbank entry BAB63125. Gaps in the human sequence indicate the likely presence of alternative exo ns that may undergo alternative splicing. This hypothesis was supported by exon mapping in both the mouse and rat genome sequences (data not shown). We were unable to detect additional exons in the mouse genomic sequence that might encode the N-terminal sequences in the human protein sequence. The similarity to the hamster clone is underlined.
Mentions: This clone encodes an ORF of 67 amino acids whose mRNA was specifically detected in hamster testis RNA (figure 1). Genome comparisons revealed strong similarities with regions of human chromosome 11, mouse chromosome 9 and rat chromosome 8 (Table 2). This clone matches to hypothetical proteins recently added to the annotation of the human and mouse genomes (FLJ13386 and XP_134746) as well as a protein encoded by a macaque cDNA (BAB63125). The alignment in figure 9 accounts for each of these clones as well as additional exons predicted in the mouse from inter-genome comparisons. The encoded protein contains several predicted coiled-coil regions but no other identifiable functional domains (figure 2).

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