| HMMscan | nr | KOG | KEGG | PDB | ITAG2.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| SNP ID | Array type ( I: Infinium G: Goldengate) |
Chromosome | Position on the SL2.40 | Location | IUPAC | SNP genotype (Heinz 1706-BG) | SNP genotype (Mutation) | Strand | Codon (Heinz 1706-BG) | Codon (Mutation) | Amino acid residue (Heinz 1706-BG) | Amino acid residue (Mutation) | SNP category | ITAG gene model | Functional site | Flanking sequences on SNP | HZ (The 40 lines) | HZ (cluster 1) | HZ (cluster 2) | HZ (cluster 3) | HZ (cluster 4) | San Marzano | Rutgers | Ponderosa | Aichi First | S. lycopersicum var cerasiforme (WIR25/30) | S. lycopersicum var cerasiforme (TOMJPF00009) | Earliana | Best Of All | Money Maker | Ailsa Craig | LA925 | Fruit | Rio Grande | Marglobe | Heinz 1706-BG | Tomato Chuukanbohon Nou 9 | Furikoma | Tomato Chuukanbohon Nou 11 | Reika | Momotaro 8 | Labell | Matrix | Geronimo | Micro-Tom_AM | Micro-Tom TGRC (LA3911) | Micro-Tom_MM | Micro-Tom | Micro-Tom NBRP (TOMJPF00001) | M82_MM | M82 | Regina | Sweet100 | S. pimpinellifolium (TOMJPF00012) | S. pimpinellifolium (LS1513) | S. pimpinellifolium (PI344102) | S. chilense (LA1958) | S. peruvianum (WIR2020) | S. peruvianum (TOMJPF00010) | S. pennellii (TOMJPF00008) | S. pennellii (LA716) | E-value | Model | HMMscan definition | nr definition | Product (KDRI) | E-value | Length% | Identity% | Positive% | KOG id | KOG No. | KOG definition | E-value | Length% | Identity% | Positive% | KO | E-value | Length% | Identity% | Positive% | Gene name [structural model (tomato)] (Structures with links can be browsed by Jmol.) |
PDB id | PDB definition | E-value | Length% | Identity% | Positive% | ITAG (interpro) |
| 6511_681 | G | SL2.40ch00 | 6691885 | exon | R | G | A | - | Ctg | Ttg | L | L | sSNP | Solyc00g007070.2.1 | # | TCCCCTCCACCTCGTCCAAAGAGGGCCCAGAACAAAGATCAAATGGAGTACACAGAGATA[T/C]TGAAGATGCGCGGTCTCCCTTACCGTTGTAAGAAATCTGATATCCTCAAGTTTTTTGGTG | 0.25 | 0 | 0 | 0 | 0 | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | TT | TT | CC | TT | CC | TT | - | - | - | gi|255561415|ref|XP_002521718.1| heterogeneous nuclear ribonucleoprotein, putative [Ricinus communis]gi|223539109|gb|EEF40705.1| heterogeneous nuclear ribonucleoprotein, putative [Ricinus communis] | heterogeneous nuclear ribonucleoprotein, putative | 1.00E-103 | 100.0 | 71.2 | 85.2 | A | KOG4211 | Splicing factor hnRNP-F and related RNA-binding proteins | 2.00E-77 | 93.9 | 54.5 | 68.9 | K12898_rcu-RCOM_0874330 | 1.00E-104 | 100.0 | 71.2 | 85.2 | Solyc00g007070.2.1 | 2HGM | gi|157883792|pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp Fgi|297787487|pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex With A Agggau G-Tract Rna | 3.00E-14 | 47.7 | 14.8 | 22.7 | Name=IPR012677;Note=Nucleotide-binding%2C alpha-beta plait | |||||||||||||
| 8457_756 | G | SL2.40ch00 | 6710340 | exon | M | A | C | - | ctT | ctG | L | L | sSNP | Solyc00g007100.2.1 | # | TCTAATTGGTCTAGATTATTTGCACAGGGAACTTGGAATTATTCATACAGACCTAAAACT[T/G]GAAAATGTTCTTTTACTTTCCACGATAAATGCCACAAAGGATCCAATTAGATCGGGAACA | 0.14 | 0 | 0 | 0 | 0 | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | TT | GG | GG | TT | TT | TT | TT | 3.90E-17 | Pkinase_Tyr | Protein tyrosine kinase | gi|255561431|ref|XP_002521726.1| srpk, putative [Ricinus communis]gi|223539117|gb|EEF40713.1| srpk, putative [Ricinus communis] | srpk, putative | 0 | 99.3 | 74.1 | 85.0 | T | KOG1290 | Serine/threonine protein kinase | 0 | 97.8 | 69.4 | 80.6 | K00924_ath-AT3G53030 | 1.00E-133 | 118.1 | 53.6 | 70.3 | Solyc00g007100.2.1 | 1WBP | gi|82407376|pdb|1WBP|A Chain A, Srpk1 Bound To 9mer Docking Motif Peptidegi|112489691|pdb|1WAK|A Chain A, X-Ray Structure Of Srpk1 | 4.00E-95 | 88.6 | 40.6 | 57.1 | Name=IPR011009;Note=Protein kinase-like domain | |||||||||||||
| 12902_733 | G | SL2.40ch00 | 6937582 | exon | Y | T | C | - | gaA | gaG | E | E | sSNP | Solyc00g007300.2.1 | # | AATATTGCAAGAGATGCAGAGGAATTTAGTTTATTTTCAGAGTAAAGAAGAGAAGAGGGA[A/G]GCATTAAAATTGTTAGATCTCGAAAATGTTCATTACCTGTTCGATGAATTGATTCAAAGA | 0.2 | 0 | 0 | 0 | 0 | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | AA | GG | GG | AA | AA | AA | GG | - | - | - | gi|255583434|ref|XP_002532476.1| leucine-rich repeat-containing protein, putative [Ricinus communis]gi|223527801|gb|EEF29900.1| leucine-rich repeat-containing protein, putative [Ricinus communis] | leucine-rich repeat-containing protein, putative | 0 | 102.5 | 67.5 | 82.9 | R | KOG0619 | FOG: Leucine rich repeat | 0 | 96.8 | 61.2 | 77.2 | - | - | - | - | - | Solyc00g007300.2.1 | 2O6Q | gi|122921460|pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte Receptors A29 | 6.00E-16 | 47.6 | 13.2 | 20.6 | Dbxref=SMART:SM00369;Name=Solyc00g007300.1.1-SM00369-9;Note=no description;database=SMART;length=24 | |||||||||||||
| 12730_421 | G | SL2.40ch00 | 12609729 | 3utr | K | G | T | - | # | # | # | # | uSNP | Solyc00g030520.2.1 | # | AAGCTGAATTGCAGATCACTGGTGATCTAGGCAAAAGCTTTAGCAAACAAAGCAGATCAA[A/C]ATTATGTTTATGAACAAGTTGTTTTTATCCCCAGTGGTTTTGTAGCACTAGAAGAACAAT | 0.17 | 0 | 0 | 0.18 | 0 | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | CC | AC | CC | CC | CC | CC | AA | AA | CC | CC | CC | CC | - | - | - | gi|255563175|ref|XP_002522591.1| Endoplasmic reticulum-Golgi intermediate compartment protein, putative [Ricinus communis]gi|223538182|gb|EEF39792.1| Endoplasmic reticulum-Golgi intermediate compartment protein, putative [Ricinus communis] | Endoplasmic reticulum-Golgi intermediate compartment protein, putative | 1.00E-44 | 79.3 | 34.4 | 38.6 | U | KOG2667 | COPII vesicle protein | 2.00E-41 | 120.3 | 31.1 | 36.1 | - | - | - | - | - | Solyc00g030520.2.1 | - | - | - | - | - | - | Name=IPR012936;Note=Protein of unknown function DUF1692 | |||||||||||||
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