title: Computational and experimental analyses reveal previously undetected coding exons of the KRIT1 (CCM1) gene.
abstract: A notable difficulty in annotating genomic sequence is identifying the correct start codon in a gene. An important such case has been found with KRIT1, the cerebral cavernous malformation type 1 (CCM1) gene. Analysis of human and mouse genomic sequence encompassing the region containing KRIT1/Krit1 using exon/gene-prediction and comparative alignment programs revealed putative exons upstream of the previously described first exon. These additional candidate exons show significant matches to mouse and human ESTs that are contiguous with and extend upstream from the previously designated 5' end of the KRIT1 cDNA sequence. RT-PCR and 5'RACE experiments confirm the presence of four additional upstream coding exons that encode an additional 207 amino acids. Importantly, a novel frameshift mutation in one of these newly identified KRIT1 exons has been found in a CCM1 family. These data establish the authentic KRIT1 amino acid sequence and suggest that the additional KRIT1 exons may harbor mutations in other CCM1 families. In addition, these results provide another example of the utility of rigorous computational and comparative sequence analysis for refining gene structure.
authors.affiliation: Department of Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA.
authors.forename: T
authors.initials: T
authors.lastname: Sahoo
authors.forename: E
authors.initials: E
authors.lastname: Goenaga-Diaz
authors.forename: I G
authors.initials: IG
authors.lastname: Serebriiskii
authors.forename: J W
authors.initials: JW
authors.lastname: Thomas
authors.forename: E
authors.initials: E
authors.lastname: Kotova
authors.forename: J G
authors.initials: JG
authors.lastname: Cuellar
authors.forename: J M
authors.initials: JM
authors.lastname: Peloquin
authors.forename: E
authors.initials: E
authors.lastname: Golemis
authors.forename: F
authors.initials: F
authors.lastname: Beitinjaneh
authors.forename: E D
authors.initials: ED
authors.lastname: Green
authors.forename: E W
authors.initials: EW
authors.lastname: Johnson
authors.forename: D A
authors.initials: DA
authors.lastname: Marchuk
mesh_terms: D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D018076:DNA, Complementary / Q000378:metabolism; D005091:Exons; D020224:Expressed Sequence Tags; D016368:Frameshift Mutation; D006801:Humans; D000075927:KRIT1 Protein; D051379:Mice; D008869:Microtubule-Associated Proteins; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation; D011518:Proto-Oncogene Proteins / Q000737:chemistry / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D018076:DNA, Complementary; D000075927:KRIT1 Protein; C107928:KRIT1 protein, human; C491535:Krit1 protein, mouse; D008869:Microtubule-Associated Proteins; D011518:Proto-Oncogene Proteins