Limits...
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.

Show MeSH

Related in: MedlinePlus

Alignment of human, macaque, mouse and rat KIF27 sequences. The derived amino acid sequences of human, macaque, mouse and rat KIF27 were aligned using the AlignX program from the Vector NTI suite of sequence analysis programs. The KIF27A sequence from human is shown and identical amino acids within the orthologous proteins are indicated with a dash. Gaps are indicated as spaces within the sequence. The motor domain is indicated with a red underline, the neck domain with a blue underline and the topoisomerase domain with a green underline. The segment corresponding to the original hamster clone is indicated with a red dotted underline. Key: Hs: homo sapiens; Mf: macaca fascicularis; Mm: mus musculus; Rn: rattus norvegicus.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC161800&req=5

Figure 4: Alignment of human, macaque, mouse and rat KIF27 sequences. The derived amino acid sequences of human, macaque, mouse and rat KIF27 were aligned using the AlignX program from the Vector NTI suite of sequence analysis programs. The KIF27A sequence from human is shown and identical amino acids within the orthologous proteins are indicated with a dash. Gaps are indicated as spaces within the sequence. The motor domain is indicated with a red underline, the neck domain with a blue underline and the topoisomerase domain with a green underline. The segment corresponding to the original hamster clone is indicated with a red dotted underline. Key: Hs: homo sapiens; Mf: macaca fascicularis; Mm: mus musculus; Rn: rattus norvegicus.

Mentions: Conceptual translation of the predicted full-length human mRNA revealed a 1401 amino acid protein that is highly conserved in macaque, mouse and rat (figures 2 and 4). Database searches revealed that it encodes a previously unreported member of the kinesin superfamily. The kinesin superfamily in humans and mice is comprised of at least 45 members, designated with the prefix KIF [26]. Based on this naming system we have assigned the name KIF27 to this new family member with the suffixes A, B and C to designate the splice variants described above (figure 3B). Domain mapping within KIF27 revealed an amino terminal kinesin motor domain and a putative topisomerase domain located in the center of the protein (figure 2 and 3B). Phylogenic analysis revealed that KIF27 belongs to the N-5 phylogenic group of KIFs [26], which includes mouse KIF21A and 21B, and human KIF4 (a group also known as the chromokinesins). Comparisons with the other members of the N-5 subgroup revealed greatest similarity within the motor domain (47–50% identity) (figure 5). In addition, the sequence of the neck domain of KIF27 located at the C-terminal end of the motor domain conformed to the consensus sequence for the neck domain of chromokinesins (figure 3B) [27].


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 KIF27 sequences. The derived amino acid sequences of human, macaque, mouse and rat KIF27 were aligned using the AlignX program from the Vector NTI suite of sequence analysis programs. The KIF27A sequence from human is shown and identical amino acids within the orthologous proteins are indicated with a dash. Gaps are indicated as spaces within the sequence. The motor domain is indicated with a red underline, the neck domain with a blue underline and the topoisomerase domain with a green underline. The segment corresponding to the original hamster clone is indicated with a red dotted underline. Key: Hs: homo sapiens; Mf: macaca fascicularis; Mm: mus musculus; Rn: rattus norvegicus.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC161800&req=5

Figure 4: Alignment of human, macaque, mouse and rat KIF27 sequences. The derived amino acid sequences of human, macaque, mouse and rat KIF27 were aligned using the AlignX program from the Vector NTI suite of sequence analysis programs. The KIF27A sequence from human is shown and identical amino acids within the orthologous proteins are indicated with a dash. Gaps are indicated as spaces within the sequence. The motor domain is indicated with a red underline, the neck domain with a blue underline and the topoisomerase domain with a green underline. The segment corresponding to the original hamster clone is indicated with a red dotted underline. Key: Hs: homo sapiens; Mf: macaca fascicularis; Mm: mus musculus; Rn: rattus norvegicus.
Mentions: Conceptual translation of the predicted full-length human mRNA revealed a 1401 amino acid protein that is highly conserved in macaque, mouse and rat (figures 2 and 4). Database searches revealed that it encodes a previously unreported member of the kinesin superfamily. The kinesin superfamily in humans and mice is comprised of at least 45 members, designated with the prefix KIF [26]. Based on this naming system we have assigned the name KIF27 to this new family member with the suffixes A, B and C to designate the splice variants described above (figure 3B). Domain mapping within KIF27 revealed an amino terminal kinesin motor domain and a putative topisomerase domain located in the center of the protein (figure 2 and 3B). Phylogenic analysis revealed that KIF27 belongs to the N-5 phylogenic group of KIFs [26], which includes mouse KIF21A and 21B, and human KIF4 (a group also known as the chromokinesins). Comparisons with the other members of the N-5 subgroup revealed greatest similarity within the motor domain (47–50% identity) (figure 5). In addition, the sequence of the neck domain of KIF27 located at the C-terminal end of the motor domain conformed to the consensus sequence for the neck domain of chromokinesins (figure 3B) [27].

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