Computational Research IIT@SEMM: AnnotateGenomicRegions
Credits
Credits: Computational Research IIT@SEMM. Copyright 2011-2014 by IIT@SEMM. All rights reserved. Developed using JSF and PrimeFaces
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Annotation History
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Step 1: Choose annotation release and genome assembly.

Releases
  • May2014
  • Sept2013
  • Oct2012
  • Sept2011
  • March2011
Genome assemblies
  • hg38
  • hg19
  • hg18
  • mm10
  • mm9
  • mm8
  • danRer7
  • sacCer3
  • sacCer2

Step 2: Choose annotation of interest.

When selected reports all matching annotations. When unselected reports only first matching annotation.
report muliple hits
annotationoverlapneighbor
refgene_TSSpm1kb_Symbol
returns UCSC refGene TSS plus/minus 1kb identified by symbol
all_mRNA_TSSpm1kb_ACC
returns accession number for UCSC all_mrna plus/minus 1kb around the TSS
refgene_Symbol
returns UCSC refGene identified by Symbol
ensGene
returns UCSC ensGene transcripts identified by ENSG and ENST identifiers
all_mRNA_ACC
returns accession number for UCSC all_mrna transcripts
cpgIslandExt
returns UCSC CpG islands
refgene_TSSpm1kb_ID
returns UCSC refGene TSS plus/minus 1kb identified by NM_ identifier
ensGene_TSSpm1kb
returns UCSC ensGene TSS plus/minus 1kb identified by ENSG and ENST identifiers
refgene_ID
returns UCSC refGene identified by NM_ identifier

Step 3: Paste or upload genomic regions to annotate and submit.

Paste for example
chr1:7577506-7577606
Chr2:7,577,506-7,577,606
CHR3:7577506-7,577,606
or white space separated
chr1 7577506 7577606
Chr2 7,577,506 7,577,606
CHR3 7577506 7,577,606
Paste example regions
Clear current regions
Submit regions
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