Just FYI, I ran J01415 through tRNAscan-SE (http://lowelab.ucsc.edu/cgi-bin/tRNAscan-SE.cgi) and Rfam (http://rfam.sanger.ac.uk/). I also looked at the pre-computed Rfam result. All three place tRNA-Gln at 4329 - 4400.
Why Do Genbank And Refseq Have Different Coordinates For Mitochondrial Features?
Why are there two different start sites for the tRNA-Gln, for instance:
http://www.ncbi.nlm.nih.gov/nuccore/V00662
tRNA complement(4320..4400)
/product="tRNA-Gln"
http://www.ncbi.nlm.nih.gov/nuccore/NC_012920
tRNA complement(4329..4400)
/gene="TRNQ"
/gene_synonym="MTTQ"
/product="tRNA-Gln"
/note="NAR: 0597"
/anticodon=(pos:complement(4365..4367),aa:Gln)
/codon_recognized="CAA"
/db_xref="GeneID:4572"
/db_xref="HGNC:7495"
/db_xref="MIM:590030"
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Neilfws
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Jeremy Leipzig
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Jeremy Leipzig
1 answer
Sequences are re-annotated over time and GenBank archives all submissions, even those that are corrected later.
The first record is an old GenBank sequence (2006). The second is a newer reference sequence (2010), with a higher degree of curation. The COMMENT section states that it was derived from another GenBank record, J01415 (2008), in which the tRNA-Gln coordinates match the RefSeq record.
I'd speculate that tRNA-finding algorithms have improved over time and/or the curators found additional biological evidence which led them to change the start site by 3 codons.
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