Gephebase

Gephebase Search Results

This Summary Table shows only the major fields for each entry. If you are interested in other fields (gene synonyms, GO terms, molecular details of the mutation, comments, etc.), please export the .csv file, which contains the complete data for each entry. Please click on a GepheID if you want to see all information regarding a particular entry.

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Your research retrieved 23 results.

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Gene	Trait	Mutation	Taxon B	Taxonomic Status	Evidence	Main Reference	Gephe ID	UniProtKB	Trait Category	Mutation Details	Taxon A	Taxon B	Edit Gene-GePhe	Taxon B	Status
Brix9-2-5/LIN5 invertase	Fruit sugar content	Unknown, Unknown	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Fridman E; Carrari F; Liu YS ; et al. (2004) Zooming in on a quantitative trait for tomato yield using interspecific introgressions.	GP00000159	LIN5 P93199	Physiology	Not identified	Solanum pennellii (species)	Solanum lycopersicum tomato - (species) D	Brix9-2-5/LIN5 invertase	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
Cf-2.1 and Cf-2.2	Pathogen resistance (leaf mold fungus ; root parasitic nematode)	Gene Loss, Deletion N	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Dixon MS; Jones DA; Keddie JS ; et al. (1996) The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat[...] 2 Additional References Dixon MS; Hatzixanthis K; Jones DA (1998) The tomato Cf-5 disease resistance gene and six homologs show pronounced allelic variation in leucin[...] Lozano-Torres JL; Wilbers RH; Gawronski P (2012) Dual disease resistance mediated by the immune receptor Cf-2 in tomato requires a common virulence t[...]	GP00000180	Q41398	Physiology	loss of the two genes Cf-2.1 and Cf-2.2 (see Dixon et al. 1998) in cultivated tomato - resistance re-acquired from related species N	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species) D	Cf-2.1 and Cf-2.2	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
Cf-4/9	Pathogen resistance	Gene Loss, Complex Change	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Parniske M; Hammond-Kosack KE; Golstein C ; et al. (1997) Novel disease resistance specificities result from sequence exchange between tandemly repeated genes[...]	GP00000181	Cf-4A Q7DLS4	Physiology	partial loss of two gene coding regions located in tandem; resulting in a chimeric gene	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species)	Cf-4/9	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
CLV3	Fruit size	Cis-regulatory, Inversion	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Xu C; Liberatore KL; MacAlister CA ; et al. (2015) A cascade of arabinosyltransferases controls shoot meristem size in tomato.	GP00001565	CLV3 Q9XF04	Morphology	A 294 kb inversion with a breakpoint 1 kb upstream of CLV3	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species) D	CLV3	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
fasciated	Fruit size Fruit architecture	Cis-regulatory, Unknown	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Cong B; Barrero LS; Tanksley SD (2008) Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during t[...]	GP00000305	fasciated B2YHV8	Morphology Morphology	Possibly 7-bp and 6- to 8-kb insertion in the first intron	Solanum pennellii (species)	Solanum lycopersicum tomato - (species)	fasciated	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
FW2.2	Fruit size	Cis-regulatory, Unknown	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Frary A; Nesbitt TC; Grandillo S ; et al. (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. 1 Additional References Nesbitt TC; Tanksley SD (2002) Comparative sequencing in the genus Lycopersicon. Implications for the evolution of fruit size in th[...]	GP00000383	ORFX Q9LKV7	Morphology	Not identified	Lycopersicon (subgenus)	Solanum lycopersicum tomato - (species)	FW2.2	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
LeSPL-CNR	Fruit ripening	Cis-regulatory, Epigenetic Change	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Manning K; Tör M; Poole M ; et al. (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibit[...]	GP00000539	101256245 Q0PY35	Physiology	Stable methylation in a 286bp region of the promoter	Solanum cheesmaniae (species)	Solanum lycopersicum tomato - (species) D	LeSPL-CNR	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
Mi1.2	Pathogen resistance (parasite)	Unknown, Unknown	Solanum lycopersicum tomato - (species)	Intraspecific	Linkage Mapping	Rossi M; Goggin FL; Milligan SB ; et al. (1998) The nematode resistance gene Mi of tomato confers resistance against the potato aphid. 2 Additional References Seah S; Yaghoobi J; Rossi M (2004) The nematode-resistance gene, Mi-1, is associated with an inverted chromosomal segment in susceptibl[...] Vos P; Simons G; Jesse T (1998) The tomato Mi-1 gene confers resistance to both root-knot nematodes and potato aphids.	GP00000655	Mi-1.2 O81137	Physiology	Not identified	Solanum peruvianum (species)	Solanum lycopersicum tomato - (species)	Mi1.2	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
MLO1	Pathogen resistance	Coding, Deletion N	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Bai Y; Pavan S; Zheng Z ; et al. (2008) Naturally occurring broad-spectrum powdery mildew resistance in a Central American tomato accession [...]	GP00000674	MLO P93766	Physiology	19bp deletion resulting in frameshift N	Solanum lycopersicum tomato - (species)	Solanum lycopersicum tomato - (species) D	MLO1	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
OVATE	Fruit shape	Coding, SNP N	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Liu J; Van Eck J; Cong B ; et al. (2002) A new class of regulatory genes underlying the cause of pear-shaped tomato fruit.	GP00000815	Q8GSM4	Morphology	V164* caused by G>T; which leads to a 75-aa truncation in the C terminus of the predicted protein N	Solanum lycopersicum tomato - (species)	Solanum lycopersicum tomato - (species)	OVATE	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
PG	Fruit ripening	Coding, Deletion N	Capsicum annuum (species) D	Domesticated	Candidate Gene	Kim S; Park M; Yeom SI ; et al. (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum speci[...]	GP00001448	PG B9VRK6	Physiology	a partial deletion of about 90aa in the C-terminal region N	Solanum lycopersicum tomato - (species)	Capsicum annuum (species) D	PG	Capsicum annuum (species)	Published - Accepted by Curator
PG	Fruit ripening	Coding, SNP N	Capsicum chinense (species) D	Domesticated	Candidate Gene	Kim S; Park M; Yeom SI ; et al. (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum speci[...]	GP00001449	PG B9VRK6	Physiology	a point mutation in the 3' splice acceptor site of intron VIII generates a premature stop codon N	Solanum lycopersicum tomato - (species)	Capsicum chinense (species) D	PG	Capsicum chinense (species)	Published - Accepted by Curator
phytochrome A-associated F-box protein	Circadian rhythm (phase)	Coding, Deletion	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Müller NA; Wijnen CL; Srinivasan A ; et al. (2016) Domestication selected for deceleration of the circadian clock in cultivated tomato.	GP00001287	101247753 K4CV85	Physiology	3bp deletion in CDS causing a 'K (lysine) loss in the highly conserved C terminus of EID1	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species) D	phytochrome A-associated F-box protein	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
phytoene synthase	Carotenoid content (fruit)	Coding, Insertion N	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Fray RG; Grierson D (1993) Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequen[...] 1 Additional References Gilbert C; Feschotte C (2018) Horizontal acquisition of transposable elements and viral sequences: patterns and consequences.	GP00001718	PSY1 P49085	Physiology	insertion of a Rider transposable element within the coding region N	Solanum lycopersicum tomato - (species)	Solanum lycopersicum tomato - (species) D	phytoene synthase	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
phytoene synthase	Carotenoid content (fruit)	Coding, Indel N	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Fray RG; Grierson D (1993) Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequen[...] 1 Additional References Gilbert C; Feschotte C (2018) Horizontal acquisition of transposable elements and viral sequences: patterns and consequences.	GP00001719	PSY1 P49085	Physiology	r y cDNA was found to be mutated at its 3' end, lacking the last 237 bases of PSY1 coding sequence and containing 185 nucleotides of an unrelated sequence in its place N	Solanum lycopersicum tomato - (species)	Solanum lycopersicum tomato - (species) D	phytoene synthase	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
Pto	Pathogen resistance	Unknown, Unknown	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Martin GB; Brommonschenkel SH; Chunwongse J ; et al. (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato.	GP00000937	pto P93215	Physiology	Not identified	Solanum lycopersicum tomato - (species)	Solanum lycopersicum tomato - (species)	Pto	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
ripening inhibitor (rin) = LeMADS-RIN and LeMADS-MC	Fruit ripening	Gene Loss, Deletion	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Vrebalov J; Ruezinsky D; Padmanabhan V ; et al. (2002) A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. 1 Additional References Giovannoni JJ; Noensie EN; Ruezinsky DM (1995) Molecular genetic analysis of the ripening-inhibitor and non-ripening loci of tomato: a first step i[...]	GP00000990	MADS-RIN Q8S4L4	Physiology	2.6kb deletion of the region located between gene LeMADS-RIN and gene LeMADS-MC; resulting in a chimeric mRNA that contains both LeMADS-RIN and LeMADS-MC coding regions.	Solanum lycopersicum tomato - (species)	Solanum lycopersicum tomato - (species) D	ripening inhibitor (rin) = LeMADS-RIN and LeMADS-MC	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
SELF PRUNING 5G (SP5G)	Flowering time	Cis-regulatory, Unknown	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Soyk S; Müller NA; Park SJ ; et al. (2017) Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato.	GP00001564	SP5G Q84XK9	Physiology	several candidate SNPs and structural variants	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species)	SELF PRUNING 5G (SP5G)	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
self-pruning (sp)	Vegetative/Reproductive state switch	Coding, SNP	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Pnueli L; Carmel-Goren L; Hareven D ; et al. (1998) The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristem[...]	GP00001035	SP O82088	Morphology	P76L due to CCT->CTT	Solanum lycopersicum tomato - (species)	Solanum lycopersicum tomato - (species) D	self-pruning (sp)	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
SlMYBATV	Coloration (anthocyanin accumulation in fruits)	Coding, Insertion N	Solanum cheesmaniae (species) D	Intraspecific	Linkage Mapping	Cao X; Qiu Z; Wang X ; et al. (2017) A putative R3 MYB repressor is the candidate gene underlying atroviolacium, a locus for anthocyanin [...]	GP00001906	CPC O22059	Morphology; Physiology	SlMYBATV encodes a R3 MYB transcription factor. 4-bp insertion predicted to result in a frame-shift that would alter the protein sequence from amino-acid position 20 onwards by inducing premature termination of translation including the R3/bHLH-binding domain N	Solanum lycopersicum tomato - (species)	Solanum cheesmaniae (species) D	SlMYBATV	Solanum cheesmaniae (species)	Published - Accepted by Curator
Style2.1	Flower morphology (style length) Autogamy	Cis-regulatory, Unknown	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Chen KY; Cong B; Wing R ; et al. (2007) Changes in regulation of a transcription factor lead to autogamy in cultivated tomatoes.	GP00001081	100301942 B6CG44	Morphology Physiology	Not identified	Solanum pennellii (species)	Solanum lycopersicum tomato - (species) D	Style2.1	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
SUN	Fruit shape	Gene Amplification, Complex Change	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Xiao H; Jiang N; Schaffner E ; et al. (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit.	GP00001084	100147716 B1N669	Morphology	Gene duplication	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species)	SUN	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
VTE3(1)	Vitamin-E synthesis	Cis-regulatory, Epigenetic Change	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Quadrana L; Almeida J; Asís R ; et al. (2014) Natural occurring epialleles determine vitamin E accumulation in tomato fruits.	GP00001684	VTE3 Q9LY74	Physiology		Solanum lycopersicum tomato - (species)	Solanum lycopersicum tomato - (species)	VTE3(1)	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator