Schema for Exoniphy - Exoniphy Mouse/Rat/Human/Dog
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Database: mm9 Primary Table: exoniphy Row Count: 172,859   Data last updated: 2007-09-05
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 609 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | chr8.56500001.9 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | - | char(1) | values | + or - for strand |
txStart | 3206102 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 3207049 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 3206102 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 3207049 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 1 | int(10) unsigned | range | Number of exons |
exonStarts | 3206102, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 3207049, | longblob | | Exon end positions (or start positions for minus strand item) |
id | 76974 | int(10) unsigned | range | |
name2 | chr8.56500001.9 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
cdsStartStat | incmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
cdsEndStat | cmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
exonFrames | 1, | longblob | | Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region. |
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Sample Rows
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bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | id | name2 | cdsStartStat | cdsEndStat | exonFrames |
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609 | chr8.56500001.9 | chr1 | - | 3206102 | 3207049 | 3206102 | 3207049 | 1 | 3206102, | 3207049, | 76974 | chr8.56500001.9 | incmpl | cmpl | 1, |
611 | chr8.56400001.4 | chr1 | - | 3411782 | 3411982 | 3411782 | 3411982 | 1 | 3411782, | 3411982, | 76973 | chr8.56400001.4 | incmpl | incmpl | 2, |
612 | chr8.56100001.13 | chr1 | - | 3660632 | 3661012 | 3660632 | 3661012 | 1 | 3660632, | 3661012, | 76972 | chr8.56100001.13 | incmpl | incmpl | 0, |
612 | chr8.56100001.11 | chr1 | - | 3662763 | 3662775 | 3662763 | 3662775 | 1 | 3662763, | 3662775, | 76971 | chr8.56100001.11 | incmpl | incmpl | 1, |
615 | chr8.55900001.9 | chr1 | - | 3997736 | 3997818 | 3997736 | 3997818 | 1 | 3997736, | 3997818, | 76970 | chr8.55900001.9 | incmpl | incmpl | 1, |
615 | chr8.55900001.8 | chr1 | - | 4009150 | 4009184 | 4009150 | 4009184 | 1 | 4009150, | 4009184, | 76969 | chr8.55900001.8 | incmpl | incmpl | 0, |
615 | chr8.55900001.7 | chr1 | - | 4014816 | 4014971 | 4014816 | 4014971 | 1 | 4014816, | 4014971, | 76968 | chr8.55900001.7 | incmpl | incmpl | 1, |
615 | chr8.55900001.2 | chr1 | - | 4032114 | 4032188 | 4032114 | 4032188 | 1 | 4032114, | 4032188, | 76967 | chr8.55900001.2 | incmpl | incmpl | 0, |
616 | chr8.55800001.16 | chr1 | - | 4082697 | 4082861 | 4082697 | 4082861 | 1 | 4082697, | 4082861, | 76966 | chr8.55800001.16 | incmpl | incmpl | 1, |
616 | chr8.55800001.11 | chr1 | - | 4110095 | 4110154 | 4110095 | 4110154 | 1 | 4110095, | 4110154, | 76965 | chr8.55800001.11 | incmpl | incmpl | 2, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Exoniphy (exoniphy) Track Description
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Description
The exoniphy program identifies evolutionarily conserved protein-coding
exons in a multiple alignment using a phylogenetic hidden Markov
model (phylo-HMM), a statistical model that simultaneously
describes exon structure and exon evolution. This track shows exoniphy
predictions for the human Mar. 2006 (hg18), mouse Feb. 2006 (mm8), rat
Nov. 2004 (rn4), and dog May 2005 (canFam2) genomes, as aligned by the
multiz program. For this track, only alignments on the "syntenic net"
between human and each other species were considered.
The predictions for mouse Feb. 2006 (mm8) were lifted to
the mouse Jul. 2007 (mm9) genome.
Methods
For a description of exoniphy, see Siepel et al. (2004).
Multiz is described in Blanchette et al. (2004).
The alignment chaining methods behind the "syntenic net" are
described in Kent et al. (2003).
Acknowledgments
Thanks to Brona Brejova of Cornell University for producing these predictions.
References
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM,
Baertsch R, Rosenbloom K, Clawson H, Green ED, et al.
Aligning multiple genomic sequences with the threaded blockset aligner.
Genome Res. 2004 Apr;14(4):708-15.
PMID: 15060014; PMC: PMC383317
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
Evolution's cauldron:
duplication, deletion, and rearrangement in the mouse and human genomes.
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.
PMID: 14500911; PMC: PMC208784
Siepel A, Haussler D.
Computational identification of evolutionarily conserved
exons.
Proc. 8th Int'l Conf. on Research in Computational Molecular Biology,
177-186 (2004).
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