Open Genome Location

Open Genome Location

You can enter a desired location in Current Range field. Mouse click the field or use Main Menu | Navigation | Open Location ... action.

Open Chromosome Range

• Enter chromosome name or chromosome location

  Supported formats:

  • chrName, e.g. chr1, chrX
  • chrName:startOffest-EndOffset, e.g. chr15:78764388-78966532, chr1:0-197195432

• Press Enter / Return keyboard key or click Go button

Open Gene Name

• Enter gene name or Ensembl gene id, e.g. cd19 or ENSG00000177455.

  All gene names from Ensembl GTF genes markup are supported. How to find which GTF file is used see in Genes Track View section.

• Press Enter / Return keyboard key or click Go button As as result cd19 gene will be shown and all other genes will be grayed out

  

  Press Esc keyboard key to make other genes not grayed.

If you get warning Unknown location try some alternative gene name, e.g use GeneCards to find aliases.

Example: "CD16" gene name isn't supported.

According to GeneCards CD16 Gene is also known as FCGR3A and ENSG00000203747.

Gene Name Auto-Completion

JBR can auto-complete Gene name using its prefix.

• Enter gene prefix, e.g. "act"

• Press Ctrl+Enter keyboard keys combination

  

• Select gene name (e.g. actbp1) using mouse or ↑ ↓ keyboard keys and then Enter / Return

• Press Enter / Return keyboard key or click Go button

Multiple Locations Mode

You can view several genome regions side by side in JBR browser.

• Enter several genes or chromosome ranges names. Items should be comma, semicolon or space separated.

  Example:

  • actb, cd19, cd14, FCGR3A
  • actb; cd19; cd14; FCGR3A
  • actb cd19 cd14 FCGR3A
  • chr2, chr4:0-100222000, chr1, chr3
  • chr5:140009653-140014645,chr16:28940514-28952628, chr7:5560838-5576073

  

• Press Enter / Return keyboard key or click Go button

  

Also, you can use predefined locations sets

• genes: All genes bodies, splicing variants are grouped together
• transcript: All genes transcripts (splicing variants are considered as different locations)
• tss: All genes transcripts promoters area (transcription start site +/- 2000 bp)
• tes: All genes TES (transcription end site +/- 2000 bp)
• cds: Protein coding genes regions
• utr3, utr5: Genes transcripts UTRs
• exons, introns: All exons / introns
• repeats, non_repeats: DNA Repeats locations
• cpg_islands: CpG islands

Additionally, for TSS / TES you could specify custom upstream/downstream offset.

• tss[-2000..100]:: Is region [TSS - 2000 bp .. TSS + 100 bp], where TSS transcription start site.
• tes[500]: Is region [TES - 500 bp .. TES + 500 bp], where TES is transcription end site.

All genes aligned side by side are too long for rendering, you need to zoom in.