Schema for Exoniphy - Exoniphy Human/Mouse/Rat/Dog
  Database: hg19    Primary Table: exoniphy    Row Count: 186,601   Data last updated: 2009-12-28
Format description: A gene prediction with some additional info.
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name chr1.1.1varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 12009int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 12045int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 12009int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 12045int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 12009,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 12045,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 chr1.1.1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,longblob   Exon frame {0,1,2}, or -1 if no frame for exon

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585chr1.1.1chr1+12009120451200912045112009,12045,0chr1.1.1incmplincmpl0,
585chr1.1.2chr1+12612126971261212697112612,12697,0chr1.1.2incmplincmpl2,
585chr1.1.3chr1-14695148291469514829114695,14829,0chr1.1.3cmplincmpl1,
585chr1.1.4chr1-14969150381496915038114969,15038,0chr1.1.4incmplincmpl1,
585chr1.1.5chr1-15795158891579515889115795,15889,0chr1.1.5incmplincmpl0,
585chr1.1.6chr1-16606167651660616765116606,16765,0chr1.1.6incmplincmpl1,
585chr1.1.7chr1-16853170551685317055116853,17055,0chr1.1.7incmplincmpl0,
585chr1.1.8chr1-17232173581723217358117232,17358,0chr1.1.8incmplincmpl0,
585chr1.1.9chr1-17605177421760517742117605,17742,0chr1.1.9incmplincmpl0,
585chr1.1.10chr1-17914180611791418061117914,18061,0chr1.1.10incmplincmpl0,

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

Exoniphy (exoniphy) Track Description
 

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 Feb. 2009 (GRCh37), mouse Jul. 2007 (mm9), 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.

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 Melissa Hubisz of the Siepel lab at 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. RECOMB '04. 2004.