Schema for Human RNA Editing - Human RNA Editing from the DAtabase of RNa EDiting |
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Database: hg19 Primary Table: darned Row Count: 42,039 Data last updated: 2011-12-22
Format description: Browser extensible data
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| bin | 586 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| chromStart | 249976 | int(10) unsigned | range | Start position in chromosome |
| chromEnd | 249977 | int(10) unsigned | range | End position in chromosome |
| name | chr1.249977 | varchar(255) | values | Name of item |
| score | 1000 | int(10) unsigned | range | Optional score, nominal range 0-1000 |
| strand | - | char(1) | values | + or - |
| thickStart | 249976 | int(10) unsigned | range | Start of where display should be thick (start codon) |
| thickEnd | 249977 | int(10) unsigned | range | End of where display should be thick (stop codon) |
| itemRgb | 0 | int(10) unsigned | range | Used as itemRgb as of 2004-11-22 |
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Sample Rows
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| bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | itemRgb |
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| 586 | chr1 | 249976 | 249977 | chr1.249977 | 1000 | - | 249976 | 249977 | 0,0,0 |
| 586 | chr1 | 249984 | 249985 | chr1.249985 | 1000 | - | 249984 | 249985 | 0,0,0 |
| 586 | chr1 | 249998 | 249999 | chr1.249999 | 1000 | - | 249998 | 249999 | 0,0,0 |
| 586 | chr1 | 250035 | 250036 | chr1.250036 | 1000 | - | 250035 | 250036 | 0,0,0 |
| 586 | chr1 | 250038 | 250039 | chr1.250039 | 1000 | - | 250038 | 250039 | 0,0,0 |
| 586 | chr1 | 250068 | 250069 | chr1.250069 | 1000 | - | 250068 | 250069 | 0,0,0 |
| 586 | chr1 | 250094 | 250095 | chr1.250095 | 1000 | - | 250094 | 250095 | 0,0,0 |
| 586 | chr1 | 250132 | 250133 | chr1.250133 | 1000 | - | 250132 | 250133 | 0,0,0 |
| 586 | chr1 | 250163 | 250164 | chr1.250164 | 1000 | - | 250163 | 250164 | 0,0,0 |
| 586 | chr1 | 250168 | 250169 | chr1.250169 | 1000 | - | 250168 | 250169 | 0,0,0 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Human RNA Editing (darned) Track Description
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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
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