Schema for Yale Pseudo60 - Yale Pseudogenes based on Ensembl Release 60 |
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Database: mm9 Primary Table: pseudoYale60 Row Count: 19,082 Data last updated: 2010-12-23
Format description: A gene prediction.
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| bin | 608 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| name | PGOMOU00000255058 | varchar(255) | values | Name of gene |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| strand | + | char(1) | values | + or - for strand |
| txStart | 3044196 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 3045304 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 0 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 0 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 1 | int(10) unsigned | range | Number of exons |
| exonStarts | 3044196, | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 3045304, | longblob | | Exon end positions (or start positions for minus strand item) |
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Sample Rows
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| bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds |
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| 608 | PGOMOU00000255058 | chr1 | + | 3044196 | 3045304 | 0 | 0 | 1 | 3044196, | 3045304, |
| 609 | PGOMOU00000125763 | chr1 | - | 3224841 | 3225235 | 0 | 0 | 1 | 3224841, | 3225235, |
| 609 | PGOMOU00000126381 | chr1 | + | 3242814 | 3243317 | 0 | 0 | 1 | 3242814, | 3243317, |
| 611 | PGOMOU00000126382 | chr1 | + | 3521875 | 3522817 | 0 | 0 | 1 | 3521875, | 3522817, |
| 617 | PGOMOU00000125764 | chr1 | - | 4246318 | 4250595 | 0 | 0 | 2 | 4246318,4248919, | 4246525,4250595, |
| 619 | PGOMOU00000126383 | chr1 | + | 4512987 | 4516815 | 0 | 0 | 2 | 4512987,4514511, | 4513698,4516815, |
| 619 | PGOMOU00000125765 | chr1 | - | 4524920 | 4525367 | 0 | 0 | 1 | 4524920, | 4525367, |
| 620 | PGOMOU00000126384 | chr1 | + | 4600551 | 4601484 | 0 | 0 | 1 | 4600551, | 4601484, |
| 620 | PGOMOU00000125766 | chr1 | - | 4678011 | 4679485 | 0 | 0 | 1 | 4678011, | 4679485, |
| 620 | PGOMOU00000125767 | chr1 | - | 4682299 | 4683505 | 0 | 0 | 1 | 4682299, | 4683505, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Yale Pseudo60 (pseudoYale60) Track Description
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Description
This track shows pseudogenes identified by the Yale Pseudogene Pipeline.
Pseudogenes are defined in this analysis as genomic sequences that are
similar to known genes with various inactivating disablements (e.g., premature
stop codons or frameshifts) in their "putative" protein coding regions.
Pseudogenes are flagged as either recently processed, recently duplicated,
or of uncertain origin (either ancient fragments or resulting from a
single-exon parent). NOTE: There are 4 pseudogenes missing - these had
overlapping coordinates in the blocks representing exons and their
identifiers are:
- PGOMOU00000130313
- PGOMOU00000139101
- PGOMOU00000136201
- PGOMOU00000128816
Methods
Briefly, the protein sequences of known human genes (as annotated by Ensembl Release
60) were used to search for similarities, not overlapping with known genes.
It was determined whether the matching sequences were disabled copies of genes
based on the occurrences of premature stop codons or frameshifts. The
intron-exon structure of the functional gene was further used to infer
whether a pseudogene was recently duplicated or processed. A duplicated
pseudogene retains the intron-exon structure of its parent functional
gene, whereas a processed pseudogene shows evidence that this structure
has been spliced out. Small pseudogene sequences that cannot be confidently
assigned to either the processed or duplicated category may be ancient
fragments. Further details are in the references below.
Credits
These data were generated by the pseudogene annotation group in the
Gerstein Lab at Yale University.
References
More information is available from
Pseudogene.org.
Zhang Z, Harrison PM, Liu Y, Gerstein M.
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in
the human genome.
Genome Res. 2003 Dec;13(12):2541-58.
PMID: 14656962; PMC: PMC403796
Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M.
Integrated pseudogene annotation for human chromosome 22: evidence for transcription.
J Mol Biol. 2005 May 27;349(1):27-45.
PMID: 15876366
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