NCBI

Sequence Viewer 3.47.0

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Example cases for coordinate reporting

The NCBI Graphical Sequence Viewer (SV) is a tool for viewing biological sequence data. Following are embedded examples of the viewer with markers indicating a particular position on the sequence. To set your own marker, right-click in Sequence Viewer on the desired position and click on the menu item "Set New Marker at Position". To see additional details of the marked position, right-click on the marker and select "Marker Details".

The HGVS name is reported in the marker details table. To view examples of searching by HGVS, refer to the HGVS and SNP Search demo page.

  1. NC_000007.14: Homo sapiens chromosome 7, GRCh38.p12 Primary Assembly.
    Gene, mRNA, and CDS are shown. Marker is right after stop codon for NP_775788.2 and XP_011514133.1.
    Link to embedded view with opened marker details table

  2. NG_005895.1: Homo sapiens TSC complex subunit 2 (TSC2), RefSeqGene (LRG_487) on chromosome 16.
    Marker is at the end of the first non-coding exon
    Link to embedded view with opened marker details table;
    notice that the table shows marked positions relative to RefSeq transcript alignments.

  3. NC_000019.9 Homo sapiens chromosome 19, GRCh37.p13 Primary Assembly. Gene CEACAM20; marker at the indel position.
    The RefSeq transcripts/proteins have a 1 nt deletion relative to the genomic sequence (forward ribosomal slippage, minus strand)
    Link to embedded view with opened marker details table

  4. NC_000019.9 Homo sapiens chromosome 19, GRCh37.p13 Primary Assembly. Gene LTBP4; marker at the indel position.
    The RefSeq transcripts/proteins have a 1 nt insertion relative to the genomic sequence (backward ribosomal slippage, plus strand)
    Link to embedded view with opened marker details table

  5. NC_024459.1: Zea mays cultivar B73 chromosome 1, B73 RefGen_v3
    Markers are at the deletion, insertion, and mismatch in RefSeq transcripts compared to the genomic sequence
    Link to embedded view with opened marker details table

  6. NC_000008.11 Homo sapiens chromosome 8, GRCh38.p12 Primary Assembly. Marker is at the SNP rs41276297 position.
    Link to embedded view with opened marker details table
  7. NM_002020.4 Homo sapiens fms related tyrosine kinase 4 (FLT4), transcript variant 2, mRNA.
    Marker is located at position 1513 relative to the start of NM_002020.4 and corresponds to position 1434 on the CDS and position 478 on the encoded protein NP_002011.2
    Link to embedded view with opened marker details table
  8. NP_000928.1 DNA-directed RNA polymerase II subunit RPB1 [Homo sapiens].
    Marker is located at position 773 relative to the start of NP_000928.1
    Link to embedded view with opened marker details table