NCBI

Sequence Viewer 3.5

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Example cases for coordinate reporting


The NCBI Graphical Sequence Viewer (SV) is a general purpose tool for viewing biological sequence data. The Sequence Viewer has a very rich set of options, following are examples of sequence coordinate reporting using markers. To set your own marker, right-click in Sequence Viewer on desired position and click on menu item "Set New Marker at Position". To see coordinates of sequences and features the marker crosses right-click on the marker and click on "Marker Details".

One of details in Marker table for Human is HGVS coordinate. You can search by this coordinate, see examples at HGVS and SNP Search demo page.

  1. Genomic
    1. mRNA and CDS features present
      1. Stop codon encoding
      2. Alignment present
      3. First exon is non-coding
      4. No alignment
      5. RefSeq Gene
      6. Forward ribosomal slippage, minus strand
      7. Forward ribosomal slippage (or large gap of another nature), plus strand
      8. Backward ribosomal slippage
    2. mRNA feature w/o product
      1. mRNA feature w/o product (Genbank), mRNA without CDS
      2. mRNA feature w/o product
    3. No mRNA feature
  2. Transcript
    1. Only CDS feature present
    2. Extra mRNA feature w/o product (Genbank)
    3. No CDS, coordinate is not marked with type because sequence has empty sequence type
  3. Protein A protein sequence