NCBI

Sequence Viewer 3.3.1

Help page

Example cases for search by HGVS and SNP


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".

Every sequence example is equipped with search expressions of two types - HGVS and SNP - you can try to search for in the corresponding panel. The search is local, that is it searches for features only on the sequence displayed.

You can analyze the result of your search by looking at Marker Details, see examples of other markers at Marker Demo page

There is an ability to mention the search term in the URL of the page so that it is automatically found and displayed. There is a separate page with examples of such links.

  1. Genomic
    1. mRNA and CDS features present
      1. Stop codon encoding
        Cut and paste following terms to the search field: NC_000007.13:g.65419300 NM_173517.3:r.656 NM_173517.3:c.*23
      2. Alignment present
        Cut and paste following terms to the search field: NT_011515.12:g.1585115 NM_000394.2:r.306 NM_000394.2:c.237 NP_000385.1:p.79 rs145489509 rs872331

        You also can indicate an aligned sequence as the base for search, e.g. NG_009823.1:g.5000 .

      3. No alignment
        Cut and paste following terms to the search field: NM_173517.3:r.634 NM_173517.3:c.*1
      4. RefSeq Gene
        Cut and paste following terms to the search field: NM_001077183.1:r.1755 NM_001077183.1:c.1716+105 NP_000539.2:p.549 rs3087469
        Pay attention, that while expression NM_001009944.2:c.*1 is correct technically, you can not search by it because the feature represented by the expression is incomplete. While expressions NM_002528.5:c.1 and NM_002528.5:r.1 work, they are not reliable also because feature NM_002528.5 is partial on this RefSeq Gene sequence. The incomplete coordinates also are not reported in Marker Table for the same reason.
    2. mRNA feature w/o product
      1. mRNA feature w/o product (Genbank), mRNA without CDS
        Expressions like RP11-38J22.4-001:r.70 are unfortunately illegal, you only can search g. and p. coordinate in this case. Try BX571818.3:g.62748 or 62748. Try CAH73262.1:p.80
      2. mRNA feature w/o product
        Cut and paste following terms to the search field: CAI95603.1:p.387
  2. Transcript
    1. Only CDS feature present
      Cut and paste following terms to the search field: NM_002020.4:r.1513 NM_002020.4:c.1434 NP_002011.2:p.478
    2. Extra mRNA feature w/o product (Genbank)
      Cut and paste following terms to the search field: M11313.1:c.1985 AAA51551.1:p.662
  3. Protein A protein sequence
    Cut and paste following terms to the search field: NP_000928.1:p.773