Schema for Human RNA Editing - Human RNA Editing from the DAtabase of RNa EDiting
  Database: hg19    Primary Table: darned    Row Count: 42,039   Data last updated: 2011-12-22
Format description: Browser extensible data
fieldexampleSQL type info description
bin 586smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 249976int(10) unsigned range Start position in chromosome
chromEnd 249977int(10) unsigned range End position in chromosome
name chr1.249977varchar(255) values Name of item
score 1000int(10) unsigned range Optional score, nominal range 0-1000
strand -char(1) values + or -
thickStart 249976int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 249977int(10) unsigned range End of where display should be thick (stop codon)
itemRgb 0int(10) unsigned range Used as itemRgb as of 2004-11-22

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgb
586chr1249976249977chr1.2499771000-2499762499770,0,0
586chr1249984249985chr1.2499851000-2499842499850,0,0
586chr1249998249999chr1.2499991000-2499982499990,0,0
586chr1250035250036chr1.2500361000-2500352500360,0,0
586chr1250038250039chr1.2500391000-2500382500390,0,0
586chr1250068250069chr1.2500691000-2500682500690,0,0
586chr1250094250095chr1.2500951000-2500942500950,0,0
586chr1250132250133chr1.2501331000-2501322501330,0,0
586chr1250163250164chr1.2501641000-2501632501640,0,0
586chr1250168250169chr1.2501691000-2501682501690,0,0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Human RNA Editing (darned) Track Description
 

Description

This track provides information on RNA nucleotides that are edited after transcription and their corresponding genomic coordinates. Only post-transcriptional editing that results in small changes to the identity of a nucleic acid are included in this track; it does not include other RNA processing such as splicing or methylation. The track contains information on A-to-I (adenosine-to-inosine) and C-to-U (cytidine-to-uridine) editing that occur due to deamination by ADAR and APOBEC enzymes, respectively. Most of the data in this track are on A-to-I editing, which is known to be highly abundant in humans.

Display

Track items are colored depending on their occurrence within RNA transcripts:

  • Dark Green: 5' UTR
  • Blue: CDS
  • Red: Intron
  • Deep Pink: 3' UTR
  • Black: Other (exon/intron status is unclear or unknown)

Methods

The data were obtained from several research papers on RNA editing and were mapped to the reference genome. More information can be obtained from DARNED database.

References:

Kiran A, Baranov PV. DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics. 2010 Jul 15;26(14):1772-6. PMID: 20547637