How interpret question mark symbol strand column in GFF file?
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9 weeks ago

Hi there , I am working on transcriptome project on Solanum lycopersicum. I have download reference genome and GFF files from https://www.ncbi.nlm.nih.gov/genome/7?genome_assembly_id=1878360

While checking the GFF file I got know to there is ? symbol in the strand column

NC_007898.3 RefSeq  mRNA    227097  142099  .   ?   .   ID=rna-LyesC2p008;Parent=gene-LyesC2p008;Dbxref=GeneID:3950473;gbkey=mRNA;gene=rps12;locus_tag=LyesC2p008

Generally the strand column has either + or - value

Can anyone help me how we can interpret this?

Ref 1.http://mblab.wustl.edu/GTF2.html 2.https://asia.ensembl.org/info/website/upload/gff.html#fieldshttps://www.ncbi.nlm.nih.gov/genome/7?genome_assembly_id=1878360

3.Reference genome : https://www.ncbi.nlm.nih.gov/genome/7?genome_assembly_id=1878360

GFF transcriptome • 335 views
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Hi!

I have taken a quick look to the CDS annotations belonging to the given transcript ID with "?" strand. If you look at them, some of the CDSs are annotated with + and some with -, see:

NC_007898.3 RefSeq  CDS 227097  227210  .   -   0   ID=cds-YP_008563112.1;Parent=rna-LyesC2p008;Dbxref=Genbank:YP_008563112.1,GeneID:3950473;Name=YP_008563112.1;exception=trans-splicing;gbkey=CDS;gene=rps12;locus_tag=LyesC2p008;part=1;product=ribosomal protein S12;protein_id=YP_008563112.1;transl_table=11
NC_007898.3 RefSeq  CDS 296767  296998  .   +   0   ID=cds-YP_008563112.1;Parent=rna-LyesC2p008;Dbxref=Genbank:YP_008563112.1,GeneID:3950473;Name=YP_008563112.1;exception=trans-splicing;gbkey=CDS;gene=rps12;locus_tag=LyesC2p008;part=2;product=ribosomal protein S12;protein_id=YP_008563112.1;transl_table=11
NC_007898.3 RefSeq  CDS 142074  142099  .   +   2   ID=cds-YP_008563112.1;Parent=rna-LyesC2p008;Dbxref=Genbank:YP_008563112.1,GeneID:3950473;Name=YP_008563112.1;exception=trans-splicing;gbkey=CDS;gene=rps12;locus_tag=LyesC2p008;part=3;product=ribosomal protein S12;protein_id=YP_008563112.1;transl_table=11

My guess is that this is why the transcript is annotated with "?".

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Entering edit mode
9 weeks ago

From http://gmod.org/wiki/GFF3:

Column 7: "strand"

The strand of the feature. + for positive strand (relative to the landmark), - for minus strand, and . for features that are not stranded. In addition, ? can be used for features whose strandedness is relevant, but unknown.

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