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Human and Drosophila GABA B R2 have a related exon organization. (A) Exons containing coding sequence are indicated by fi lled boxes drawn to scale. 

Human and Drosophila GABA B R2 have a related exon organization. (A) Exons containing coding sequence are indicated by fi lled boxes drawn to scale. 

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The type B gamma-aminobutryic acid receptor (GABA(B)R) is a G protein coupled receptor that mediates slow pre- and post-synaptic inhibition in the nervous system. We find that the human GABA(B)R2 gene spans greater than 350 kb and contains 2.8 kb of coding region in 19 exons. The overall similarity in genomic structure with regard to conservation o...

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... B Rs , GABA B R3 . The Drosophila genome has fi ve chromosomes and the chromosome arms are referred to as L and R (http:// fl ybase.bio.indiana.edu). The Drosophila GABA B R genes are located on two different chromosomes: 3R ( GABA R2 ) and 2L ( GABA R1 and GABA R3 ). Drosophila GABA B R1 and human GABA B R1b share 12 intron locations. The Drosophila GABA B R1 gene contains 13 exons. Drosophila GABA B Rs do not contain sushi domains that are found in the human GABA B R1a transcript (see Fig. 10B), although sushi domain sequences exist in the The size of introns in human GABA B R1 range from 97 to 7616 bp, in human GABA B R2 they range from 2697 to 112,150 bp, and in Drosophila GABA B R2 they range from 55 to 393 bp (Table 5). Intron size has therefore not been conserved between human and Drosophila GABA Rs . Drosophila genome. Drosophila GABA B R1 and human GABA B R1b have two exons, exons 2 and 3, with an identical number of bases, of 135 and 171 bp. Drosophila GABA B R1 exons, exons 4, 7, 9, 10 and 11, each correspond to two human GABA B R1 exons. The organization of the Drosophila GABA B R2 gene was determined by comparing Drosophila cDNA and genomic sequences (Table 4, Figs. 4 and 5). An alignment of Drosophila and human GABA B R2 genes reveals eight comparable intron locations (Fig. 5). Seven Drosophila GABA B R2 exons, exons 3 – 9, have the greatest similarity to human GABA B R2 and are between 49 – 56% identical at the nucleotide level. A single Drosophila GABA B R2 exon, exon 3, corresponds to four exons in human GABA B R2 , exons 2 – 5. Similarly, Drosophila GABA B R2 exons 6 and 7 each correspond to three human GABA B R2 exons, exons 8 – 10 and 11 – 13. Three Drosophila exons, exons 3, 6 and 7, and the comparable three regions in human GABA B R2 have a similar or identical number of bases (Fig. 5). In addition, two individual Drosophila GABA B R2 exons, exons 8 and 9, contain an identical number of bases as two human exons. Most differences between the human and Drosophila 0 0 0 GABA B R2 genes are located at the 5 and 3 ends. The 5 0 end of Drosophila GABA B R2 contains an intron in the 5 UTR that was not found in the human GABA B R2 gene, based upon the longest cDNA sequence available for human 0 GABA B R2 . The 3 end of Drosophila GABA B R2 is larger 0 than the 3 end of human GABA B R2 but both genes have 0 three introns in the 3 end that encodes the C-terminus. Each of the Drosophila GABA B R2 introns match the U2-Type GT-AG intron consensus (Table 3) and 5/12 introns inter- rupt a codon. The location of introns shared by human and Drosophila GABA B R2 argues that these orthologous genes arose from a common ancestral GABA R2 gene. Three GABA B R2 isoforms differing in their C-termini have been proposed to be a result of alternative mRNA splicing of two exons in the sequence encoding the GABA B R2 C- terminus (Clark et al., 2000). We fi nd that an alignment of the reported sequence of the cDNAs with GABA B R2 genomic sequence indicates that the sequences of the proposed alternative splicing lies within one exon, exon 19 of GABA B R2 (Fig. 6). To determine whether the absence of the expected genomic structure is due to a deletion, rearrangement, or error in the genomic sequence, different GABA B R2 genomic and cDNA sequences were compared (Fig. 6). The GABA B R2 exon 19 sequence derived from four genomic clones is identical in 44 overlapping human GABA B R2 ESTs (GenBank), ten human GABA B R2 cDNAs (GenBank), and 64 human adult and fetal brain GABA B R2 cDNAs (Martin et al., 1999), except for changes in certain single nucleotides. These results indicate that the genomic clone sequence ascribed to exon 19 (Figs. 1 and 6) is a true copy of the GABA B R2 genomic DNA and that the location of the proposed GABA B R2 alternative splicing is within exon 19. These results suggest that an alternative mechanism, such as intron retention, is required to explain the generation of the proposed GABA B R2 isoforms. Intron retention (Kilpatrick et al., 1999) is a mode of pre-mRNA splicing where an intron can be spliced or retained in the mature RNA as a result of the utilization of genomic sequence as an exon with respect to one transcript and as an intron with respect to another. (GABA B R2b) and ACAGA (GABA B R2c), fl ank the deleted sequence. In consequence, there are fi ve positions for GABA B R2b and six positions for GABA B R2c to examine and determine whether splice junctions exist at these loca- 0 0 tions (Table 6). However, no 5 splice donor or 3 splice acceptor sequences (Table 2) are found in exon 19 for any of the possible intron locations consistent with the formation of GABA B R2b or GABA B R2c . The GABA B R2 genomic sequence does not contain canonical splice sites for GABA R2b or GABA R2c . To determine whether the proposed GABA B R2b and GABA B R2c transcripts could have been generated by alternative splicing we asked whether exon 19 contains appro- priately located canonical splice sites. To look for the presence of splice sites in exon 19, the cDNA sequences of GABA B R2b and GABA B R2c were aligned with the exon 19 genomic sequence (Fig. 7). 0 Surprisingly, this alignment reveals a repeated sequence 5 0 and 3 of both deletions. The repeated sequences, CCAC GABA B R1a has fi ve additional 5 exons when compared 0 to GABA B R2 . Two of the fi ve 5 GABA B R1a exons encode two sushi domains (Fig. 8). Sushi domains are not found in GABA R1b or GABA R2. Each sushi domain has ...
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... B Rs , GABA B R3 . The Drosophila genome has fi ve chromosomes and the chromosome arms are referred to as L and R (http:// fl ybase.bio.indiana.edu). The Drosophila GABA B R genes are located on two different chromosomes: 3R ( GABA R2 ) and 2L ( GABA R1 and GABA R3 ). Drosophila GABA B R1 and human GABA B R1b share 12 intron locations. The Drosophila GABA B R1 gene contains 13 exons. Drosophila GABA B Rs do not contain sushi domains that are found in the human GABA B R1a transcript (see Fig. 10B), although sushi domain sequences exist in the The size of introns in human GABA B R1 range from 97 to 7616 bp, in human GABA B R2 they range from 2697 to 112,150 bp, and in Drosophila GABA B R2 they range from 55 to 393 bp (Table 5). Intron size has therefore not been conserved between human and Drosophila GABA Rs . Drosophila genome. Drosophila GABA B R1 and human GABA B R1b have two exons, exons 2 and 3, with an identical number of bases, of 135 and 171 bp. Drosophila GABA B R1 exons, exons 4, 7, 9, 10 and 11, each correspond to two human GABA B R1 exons. The organization of the Drosophila GABA B R2 gene was determined by comparing Drosophila cDNA and genomic sequences (Table 4, Figs. 4 and 5). An alignment of Drosophila and human GABA B R2 genes reveals eight comparable intron locations (Fig. 5). Seven Drosophila GABA B R2 exons, exons 3 – 9, have the greatest similarity to human GABA B R2 and are between 49 – 56% identical at the nucleotide level. A single Drosophila GABA B R2 exon, exon 3, corresponds to four exons in human GABA B R2 , exons 2 – 5. Similarly, Drosophila GABA B R2 exons 6 and 7 each correspond to three human GABA B R2 exons, exons 8 – 10 and 11 – 13. Three Drosophila exons, exons 3, 6 and 7, and the comparable three regions in human GABA B R2 have a similar or identical number of bases (Fig. 5). In addition, two individual Drosophila GABA B R2 exons, exons 8 and 9, contain an identical number of bases as two human exons. Most differences between the human and Drosophila 0 0 0 GABA B R2 genes are located at the 5 and 3 ends. The 5 0 end of Drosophila GABA B R2 contains an intron in the 5 UTR that was not found in the human GABA B R2 gene, based upon the longest cDNA sequence available for human 0 GABA B R2 . The 3 end of Drosophila GABA B R2 is larger 0 than the 3 end of human GABA B R2 but both genes have 0 three introns in the 3 end that encodes the C-terminus. Each of the Drosophila GABA B R2 introns match the U2-Type GT-AG intron consensus (Table 3) and 5/12 introns inter- rupt a codon. The location of introns shared by human and Drosophila GABA B R2 argues that these orthologous genes arose from a common ancestral GABA R2 gene. Three GABA B R2 isoforms differing in their C-termini have been proposed to be a result of alternative mRNA splicing of two exons in the sequence encoding the GABA B R2 C- terminus (Clark et al., 2000). We fi nd that an alignment of the reported sequence of the cDNAs with GABA B R2 genomic sequence indicates that the sequences of the proposed alternative splicing lies within one exon, exon 19 of GABA B R2 (Fig. 6). To determine whether the absence of the expected genomic structure is due to a deletion, rearrangement, or error in the genomic sequence, different GABA B R2 genomic and cDNA sequences were compared (Fig. 6). The GABA B R2 exon 19 sequence derived from four genomic clones is identical in 44 overlapping human GABA B R2 ESTs (GenBank), ten human GABA B R2 cDNAs (GenBank), and 64 human adult and fetal brain GABA B R2 cDNAs (Martin et al., 1999), except for changes in certain single nucleotides. These results indicate that the genomic clone sequence ascribed to exon 19 (Figs. 1 and 6) is a true copy of the GABA B R2 genomic DNA and that the location of the proposed GABA B R2 alternative splicing is within exon 19. These results suggest that an alternative mechanism, such as intron retention, is required to explain the generation of the proposed GABA B R2 isoforms. Intron retention (Kilpatrick et al., 1999) is a mode of pre-mRNA splicing where an intron can be spliced or retained in the mature RNA as a result of the utilization of genomic sequence as an exon with respect to one transcript and as an intron with respect to another. (GABA B R2b) and ACAGA (GABA B R2c), fl ank the deleted sequence. In consequence, there are fi ve positions for GABA B R2b and six positions for GABA B R2c to examine and determine whether splice junctions exist at these loca- 0 0 tions (Table 6). However, no 5 splice donor or 3 splice acceptor sequences (Table 2) are found in exon 19 for any of the possible intron locations consistent with the formation of GABA B R2b or GABA B R2c . The GABA B R2 genomic sequence does not contain canonical splice sites for GABA R2b or GABA R2c . To determine whether the proposed GABA B R2b and GABA B R2c transcripts could have been generated by alternative splicing we asked whether exon 19 contains appro- priately located canonical splice sites. To look for the presence of splice sites in exon 19, the cDNA sequences of GABA B R2b and GABA B R2c were aligned with the exon 19 genomic sequence (Fig. 7). 0 Surprisingly, this alignment reveals a repeated sequence 5 0 and 3 of both deletions. The repeated sequences, CCAC GABA B R1a has fi ve additional 5 exons when compared 0 to GABA B R2 . Two of the fi ve 5 GABA B R1a exons encode two sushi domains (Fig. 8). Sushi domains are not found in GABA R1b or GABA R2. Each sushi domain has ...
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... organization of the Drosophila GABA B R2 gene was determined by comparing Drosophila cDNA and genomic sequences ( Table 4, Figs. 4 and 5). An alignment of Droso- phila and human GABA B R2 genes reveals eight comparable intron locations (Fig. 5). Seven Drosophila GABA B R2 exons, exons 3-9, have the greatest similarity to human GABA B R2 and are between 49-56% identical at the nucleo- tide level. A single Drosophila GABA B R2 exon, exon 3, corresponds to four exons in ...
Context 4
... organization of the Drosophila GABA B R2 gene was determined by comparing Drosophila cDNA and genomic sequences ( Table 4, Figs. 4 and 5). An alignment of Droso- phila and human GABA B R2 genes reveals eight comparable intron locations (Fig. 5). Seven Drosophila GABA B R2 exons, exons 3-9, have the greatest similarity to human GABA B R2 and are between 49-56% identical at the nucleo- tide level. A single Drosophila GABA B R2 exon, exon 3, corresponds to four exons in human GABA B R2, exons 2-5. Similarly, Drosophila GABA B R2 exons 6 and 7 each corre- spond to three human ...
Context 5
... GABA B R2 exon, exon 3, corresponds to four exons in human GABA B R2, exons 2-5. Similarly, Drosophila GABA B R2 exons 6 and 7 each corre- spond to three human GABA B R2 exons, exons 8-10 and 11- 13. Three Drosophila exons, exons 3, 6 and 7, and the comparable three regions in human GABA B R2 have a simi- lar or identical number of bases (Fig. 5). In addition, two individual Drosophila GABA B R2 exons, exons 8 and 9, contain an identical number of bases as two human ...

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... RT-qPCR was performed as described in our previous study (He et al., 2011(He et al., , 2022 We used the primers amplifying sequence from exon 2 through exon 6 of GABBR1 (NM_001470.4) to identify GABBR1a (containing 2 sushi domains on exon 3 and 4) and GABBR1c (containing 1 sushi domain on exon 3), according to previous studies (Bettler et al., 2004;Lee et al., 2010;Martin et al., 2001). Primers for human GABBR1a (product size 563 bp) and GABBR1c (product size 377 bp) were forward 5′ CAGAT CAT ACA CCC GCCCTG3′ and reverse 5′CTGTC GTG GTG GAT GAGCTT3′. ...
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