SEF1/YBL066C Locus History Help


Nomenclature History
Standard Name Reference
SEF1 Groom KR, et al.  (1998) Kluyveromyces lactis SEF1 and its Saccharomyces cerevisiae homologue bypass the unknown essential function, but not the mitochondrial RNase P function, of the S. cerevisiae RPM2 gene. Yeast 14(1):77-87
Sequence Annotation Notes
DateNote
2004-04-15Based on sequence comparisons with related fungi, Brachat et al. propose that SEF1/YBL066C contains an intron (see below). However, sequence comparisons with related Saccharomyces species (Kellis et al.) do not support this proposal because the Saccharomyces species have highly conserved amino acid sequence in the proposed "intron."

intron and splice junctions proposed by Brachat et al.: 
exon 1: ...aacgccaacg cgattggaag atcacaaagta 


intron: gtatgtccca ttcacgtaca cctttgtttc ggtcaatata tgacagttgg
        attccgcgtc cgaccccggt cctctaaaag acgggatatc cacctctgag
        ttgttccaaa gttgatatca tagaacaacg accacgattc tacgggacta
        acactgttct ctatccaacc acgataatga aaacaacgtg aagactcctg


exon 2: gaaacaaac taacggattt ttttcagc...
Kellis M, et al.  (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54
Brachat S, et al.  (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4(7):R45
2004-07-16SGD re-sequenced this region in S288C and found that 37 nucleotide insertions and 4 nucleotide changes were necessary to correct the reference sequence. As a consequence of these changes, SEF1/YBL066C was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 1,057 to 1,148 amino acids. 
New:         1 TGTTTCCAGGAGTCTTCACGTTGTTTTCATTATCGATGGTTTGGAAGTTAGAAGAAGTTA 60 
               ||||||||||||||||||||||||||||||||||| ||||| |||   ||| |||| 
Current: 96777 TGTTTCCAGGAGTCTTCACGTTGTTTTCATTATCG-TGGTT-GGA---TAG-AGAA---- 96826

New:        61 CAGTGTTAGTGCCCGTAGAAAATCGTTGGTTCGTTTTGTTGCTATTGATATCATTACTTT 120
               |||||||||| |||||||||  |||| || |||||  ||| ||| ||||||||  ||||| 
Current: 96827 CAGTGTTAGT-CCCGTAGAA--TCGT-GG-TCGTT--GTT-CTA-TGATATCA--ACTTT 96875

New:       121 TGGAAAACAAGCTCAGAGGTGGATATGCCGTGCTTTTAGAGGAGCCGGGGTCGGAAACGA 180
                ||||  ||| ||||||||||||||| |||| ||||||||||| |||||||||||  ||
Current: 96876 -GGAA--CAA-CTCAGAGGTGGATATCCCGT-CTTTTAGAGGA-CCGGGGTCGGA--CG- 96926

New:       181 CGGAATGCAAATCTGTCATATTATTTGACTTCGAAGCAATCGGTGTACGTGAATGGGACA 240 
               |||||| |||  ||||||||| | |||||  |||| |||  ||||||||||||||||||| 
Current: 96927 CGGAATCCAA--CTGTCATAT-A-TTGAC--CGAAACAAA-GGTGTACGTGAATGGGACA 96979
1999-04-23A change was made to the systematic sequence of Chromosome II within the ORF SEF1/YBL066C. The two nucleotides TG at positions 575 and 576 (chromosomal coordinates 97484-97485) were changed to GC, altering translation by changing amino acid 192 from Gln (CAA) to Ala (GCA). Note that this ORF is on the Crick strand. 
Old: 97441 AGAACCGTCAGAATCTCCGTTATTTGTCTTGGCTAGCTTTTCTTGCTGCTTTAAGGCATT 97500
           |||||||||||||||||||||||||||||||||||||||||||  |||||||||||||||
New: 97441 AGAACCGTCAGAATCTCCGTTATTTGTCTTGGCTAGCTTTTCTGCCTGCTTTAAGGCATT 97500
Cherry JM, et al.  (1998) "Genetic and Physical Maps of Saccharomyces cerevisiae (Edition 15)". Pp. 414-420 in 1998 Yeast Genetics and Molecular Biology Meeting Program and Abstracts. Bethesda, MD: The Genetics Society of America