The best available gene model is shown in the 'Gene Models' track. Manually reviewed gene models are shown in dark blue and dark red, while models not yet reviewed are shown in pale blue and red for Watson and Crick genes, respectively.
The Curated Models track is a track which dictyBase curators create create from experimentally derived data typically deposited in GenBank. Genes are assigned coordinates based on all available information.
Gene predictions for chromosome 2 provided by personal communication with the International consortium of the Dictyostelium Genome Project as described in "The genome of the social amoeba Dictyostelium discoideum". Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A. (2005)Nature 435(7038): 43-57. Gene predictions for chromosome 6 provided by personal communication with the International consortium of the Dictyostelium Genome Project at Baylor College of Medicine (http://dictygenome.bcm.tmc.edu/)
Gene repredictions performed by Daniel Schneider with assistance from Eric Just using the geneid software using a customized training set based on Dictyostelium curated models (Dec 2007).
This track shows regions where GenBank mRNA's align to genomic sequence. The mRNAs were blasted against the genomic sequence. The hits were filtered using an algorithm described in:
"Alignment of BLAST High-scoring Segment Pairs Based on the Longest Increasing Subsequence Algorithm" Zhang H, Bioinformatics, 19:1391-1396, 2003.
Only the longest total hit region which covers >=85% of the query seqeunce is shown.
This track shows regions where CDSs from GenBank DNA records align to genomic sequence. The CDSs were blasted against the genomic sequence. The hits were filtered using an algorithm described in:
"Alignment of BLAST High-scoring Segment Pairs Based on the Longest Increasing Subsequence Algorithm" Zhang H, Bioinformatics, 19:1391-1396, 2003.
Only the longest total hit region which covers >=85% of the query seqeunce is shown.
This track shows regions where ESTs align to genomic sequence. The ESTs are published by the Japanese cDNA project and obtained from GenBank. They were blasted against the genomic sequence. The hits were filtered using an algorithm described in:
"Alignment of BLAST High-scoring Segment Pairs Based on the Longest Increasing Subsequence Algorithm" Zhang H, Bioinformatics, 19:1391-1396, 2003.
Only the longest total hit region which covers >=75% of the query seqeunce is shown.
At low zoom level, this track shows the amino acids encoded by the genomic sequence in each of the three open reading frames. At high zoom level, stop codons are represented by a solid red line, such that open reading frames can easily be detected.
At low zoom level, this track shows the amino acids encoded by the genomic sequence in each of the three open reading frames. At high zoom level, stop codons are represented by a solid red line, such that open reading frames can easily be detected.
