71461210-c213-48d4-9a23-055976f2e53c
Report of a novel exon in CCDC50
The mouse gene Ccdc50 has two isoforms (transcript variant 1, NM_026202.4; NP_080478.2, a 305 aa-long isoform, and transcript variant 2, NM_001025615.3; NP_001020786.1, a 290 aa-short isoform), and both are expressed in the mouse cochlea at different developmental stages (E18.5, P0 and P14) (Modamio-Hoybjor et al., 2007). Recently, a novel mouse transcript variant 3 (NM_001289436.1) has been predicted that includes a new exon (exon 3b) and changes the reading frame compared with the original mouse transcript. This variant uses an alternative downstream start codon (at the 5' end of exon 7 of the long transcript) that would produce a shorter isoform (NP_001276365.1) corresponding to the last 155 aa of the long isoform. This novel exon 3b has been previously reported in the mouse (Modamio-Hoybjor et al., 2007), where it was suggested to be the penultimate exon in a novel N-terminal transcript, distinct from NM_001289436.1. During a study of the expression of Ccdc50 in the mouse inner ear, we investigated the new predicted transcript using nested PCR to amplify from cDNA. Primers designed to amplify from exon 3b generated a PCR product of the expected sizes, and Sanger sequencing confirmed the presence of exon 3b in both wildtype brain and inner ear. This experimental evidence supports the inclusion of exon 3b in the transcripts. References: Modamio-Hoybjor, S., Mencia, A., Goodyear, R., del Castillo, I., Richardson, G., Moreno, F. and Moreno-Pelayo, M. A. (2007) A mutation in CCDC50, a gene encoding an effector of epidermal growth factor-mediated cell signaling, causes progressive hearing loss. Am J Hum Genet, 80(6), 1076-89.
The mouse gene Ccdc50 has two isoforms (transcript variant 1, NM_026202.4; NP_080478.2, a 305 aa-long isoform, and transcript variant 2, NM_001025615.3; NP_001020786.1, a 290 aa-short isoform), and both are expressed in the mouse cochlea at different developmental stages (E18.5, P0 and P14) (Modamio-Hoybjor et al., 2007). Recently, a novel mouse transcript variant 3 (NM_001289436.1) has been predicted that includes a new exon (exon 3b) and changes the reading frame compared with the original mouse transcript. This variant uses an alternative downstream start codon (at the 5' end of exon 7 of the long transcript) that would produce a shorter isoform (NP_001276365.1) corresponding to the last 155 aa of the long isoform. This novel exon 3b has been previously reported in the mouse (Modamio-Hoybjor et al., 2007), where it was suggested to be the penultimate exon in a novel N-terminal transcript, distinct from NM_001289436.1. During a study of the expression of Ccdc50 in the mouse inner ear, we investigated the new predicted transcript using nested PCR to amplify from cDNA. Primers designed to amplify from exon 3b generated a PCR product of the expected sizes, and Sanger sequencing confirmed the presence of exon 3b in both wildtype brain and inner ear. This experimental evidence supports the inclusion of exon 3b in the transcripts. References: Modamio-Hoybjor, S., Mencia, A., Goodyear, R., del Castillo, I., Richardson, G., Moreno, F. and Moreno-Pelayo, M. A. (2007) A mutation in CCDC50, a gene encoding an effector of epidermal growth factor-mediated cell signaling, causes progressive hearing loss. Am J Hum Genet, 80(6), 1076-89.