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An organized view of the transcripome



Library:13025 (dbEST ID)

Normalized cDNA library from ripening tomato pericarp

Library Description

Organism:Solanum lycopersicum
Developmental stage:Turning stage of fruit ripening.
Tissue:Pericarp

Equal amounts of total RNA isolated from two tomato genotypes differing in juice Bostwick value were mixed and used to prepare a normalized cDNA library (Takahashi-N and Ko-MSH, 1994: Toward a whole cDNA catalog: construction of an equalized cDNA library from mouse embryos. Genomics-San-Diego, 23: 1, 202-210). The resultant PCR amplified products were ligated into pBluscript SKII- vector (Stratagene) and transformed into E. coli DH5alpha

Source: Handa, AK, Purdue University

Gene Content Analysis

1,355 ESTs from this library were grouped into 985 UniGene entries (putative genes) [UniGene build #38, 02-Aug-2012]. EST counts for each entry may be used to calculate an approximate expression level in transcripts per million (TPM).

ESTs TPM   UniGene Entry
14 10332 Les.85 Ethylene receptor.
10 7380 Les.3981 S-adenosylmethionine decarboxylase.
10 7380 Les.10326 Beta-fructosidase.
9 6642 Les.4346 Ss-galactosidase.
9 6642 Les.19757 Transcribed locus, moderately similar to XP_002272760.1 PREDICTED: uncharacterized protein LOC100248610 [Vitis vinifera].
8 5904 Les.2560 1-aminocyclopropane-1-carboxylate oxidase 1.
6 4428 Les.8959 Transcribed locus.
6 4428 Les.19055 Clone 113780F, mRNA sequence.
6 4428 Les.16492 Clone 132548R, mRNA sequence.
6 4428 Les.10687 Transcribed locus, weakly similar to XP_003554329.1 PREDICTED: eukaryotic translation initiation factor 3 subunit A-like [Glycine max].
5 3690 Les.9754 Uncharacterized LOC544138.
5 3690 Les.6918 Transcribed locus, strongly similar to NP_189208.1 protein phosphatase 2A subunit A2 [Arabidopsis thaliana].
5 3690 Les.3817 Alkaline alpha-galactosidase seed imbibition protein.
5 3690 Les.3627 E8 protein homolog.
5 3690 Les.3044 Transcribed locus, strongly similar to NP_849640.1 DNA-directed RNA Polymerase II subunit L [Arabidopsis thaliana].
5 3690 Les.2131 Transcribed locus, weakly similar to XP_002299684.1 predicted protein [Populus trichocarpa].
5 3690 Les.19286 Histidine decarboxylase.
5 3690 Les.19083 Ubiquitin conjugating enzyme.
5 3690 Les.10225 Fruit-specific protein.
4 2952 Les.9942 Transcribed locus, moderately similar to NP_188686.2 purple acid phosphatase 18 [Arabidopsis thaliana].
4 2952 Les.9718 Transcribed locus.
4 2952 Les.9667 Transcribed locus.
4 2952 Les.8564 Clone 113739R, mRNA sequence.
4 2952 Les.6948 Transcribed locus, moderately similar to XP_002325512.1 predicted protein [Populus trichocarpa].
4 2952 Les.4819 Clone 133556R, mRNA sequence.
4 2952 Les.3293 Transcribed locus, strongly similar to NP_568746.1 ATP-dependent Clp protease ATP-binding subunit ClpC [Arabidopsis thaliana].
4 2952 Les.2553 Transcribed locus, strongly similar to XP_002283649.1 PREDICTED: 40S ribosomal protein S21 isoform 1 [Vitis vinifera].
4 2952 Les.19260 Transcribed locus, weakly similar to XP_002269629.1 PREDICTED: long-chain-alcohol oxidase FAO4A-like [Vitis vinifera].
4 2952 Les.13761 Phytoene synthetase.
4 2952 Les.13082 Transcribed locus.
4 2952 Les.10550 Transcribed locus, moderately similar to NP_172655.1 aspartic proteinase A1 [Arabidopsis thaliana].
3 2214 Les.9725 Var. cerasiforme mRNA for cell cycle switch 52A (ccs52A gene), cultivar WVA106.
3 2214 Les.9668 Transcribed locus, weakly similar to XP_003531583.1 PREDICTED: elongation of fatty acids protein A-like [Glycine max].
3 2214 Les.8562 Transcribed locus.
3 2214 Les.8179 Type I small heat shock protein 17.6 kDa isoform.
3 2214 Les.7177 Transcribed locus.
3 2214 Les.6790 Transcribed locus, weakly similar to XP_002313391.1 predicted protein [Populus trichocarpa].
3 2214 Les.6663 Transcribed locus, weakly similar to XP_003521365.1 PREDICTED: uncharacterized protein LOC100816435 [Glycine max].
3 2214 Les.6431 Transcribed locus, weakly similar to NP_001049729.1 Os03g0278800 [Oryza sativa Japonica Group].
3 2214 Les.611 Transcribed locus, moderately similar to XP_002302795.1 predicted protein [Populus trichocarpa].
3 2214 Les.463 Transcribed locus, moderately similar to XP_002322262.1 predicted protein [Populus trichocarpa].
3 2214 Les.4548 Clone 113584R, mRNA sequence.
3 2214 Les.4531 Ethylene response factor 5.
3 2214 Les.4521 Transcribed locus, moderately similar to XP_002271791.1 PREDICTED: photosystem II 10 kDa polypeptide, chloroplastic [Vitis vinifera].
3 2214 Les.4509 Transcribed locus, moderately similar to XP_003518793.1 PREDICTED: cytochrome c oxidase subunit 5C-2 [Glycine max].
3 2214 Les.4497 Phospho-2-dehydro-3-deoxyheptonate aldolase.
3 2214 Les.4187 Non-specific lipid transfer protein.
3 2214 Les.3366 Dehydroquinate dehydratase/shikimate:NADP oxidoreductase.
3 2214 Les.3296 Transcribed locus, moderately similar to XP_002961786.1 hypothetical protein SELMODRAFT_6427 [Selaginella moellendorffii].
3 2214 Les.2726 Transcribed locus, strongly similar to NP_194222.1 protein transport protein sec61 subunit gamma-1 [Arabidopsis thaliana].
3 2214 Les.21920 1-aminocyclopropane-1-carboxylate synthase.
3 2214 Les.19348 NP24 protein precursor.
3 2214 Les.14566 Uncharacterized LOC778318.
3 2214 Les.14454 Transcribed locus, moderately similar to XP_002282721.1 PREDICTED: uncharacterized protein LOC100245396 isoform 1 [Vitis vinifera].
3 2214 Les.14309 Clone 134471R, mRNA sequence.
3 2214 Les.14019 Clone 114402R, mRNA sequence.
3 2214 Les.1401 1,4-alpha-glucan-maltohydrolase.
3 2214 Les.13652 Transcribed locus, weakly similar to NP_197131.2 cohesin complex subunit SCC1 [Arabidopsis thaliana].
3 2214 Les.13348 Transcribed locus, moderately similar to XP_002283878.1 PREDICTED: uncharacterized protein LOC100245204 [Vitis vinifera].
3 2214 Les.1298 IAA9.
3 2214 Les.12433 Transcribed locus, moderately similar to NP_181830.1 putative polyamine oxidase 2 [Arabidopsis thaliana].
3 2214 Les.11795 Transcribed locus, moderately similar to NP_001051144.1 Os03g0727900 [Oryza sativa Japonica Group].
3 2214 Les.11735 Transcribed locus, strongly similar to NP_174118.1 nuclear transport factor 2B [Arabidopsis thaliana].
3 2214 Les.11389 Transcribed locus, moderately similar to XP_002324446.1 predicted protein [Populus trichocarpa].
3 2214 Les.10060 Transcribed locus, strongly similar to XP_003556527.1 PREDICTED: topless-related protein 3-like [Glycine max].
3 2214 Les.1 Beta-galactosidase.
2 1476 Les.9902 Transcribed locus, moderately similar to XP_002315796.1 predicted protein [Populus trichocarpa].
2 1476 Les.9899 Transcribed locus, moderately similar to NP_001234339.1 bZIP DNA-binding protein [Solanum lycopersicum].
2 1476 Les.9732 Transcribed locus, weakly similar to NP_194480.2 proton pump interactor 1 [Arabidopsis thaliana].
2 1476 Les.9723 Transcribed locus, weakly similar to NP_187413.1 uncharacterized protein [Arabidopsis thaliana].
2 1476 Les.9722 Transcribed locus, weakly similar to XP_002327171.1 predicted protein [Populus trichocarpa].
2 1476 Les.9721 Transcribed locus, weakly similar to XP_002325585.1 predicted protein [Populus trichocarpa].
2 1476 Les.9720 Transcribed locus, moderately similar to NP_001119162.1 exocyst subunit exo70 family protein A1 [Arabidopsis thaliana].
2 1476 Les.9717 Transcribed locus, weakly similar to XP_002968666.1 hypothetical protein SELMODRAFT_170125 [Selaginella moellendorffii].
2 1476 Les.9716 Transcribed locus, moderately similar to XP_003626696.1 3-hydroxyisobutyryl-CoA hydrolase-like protein [Medicago truncatula].
2 1476 Les.9682 Transcribed locus, moderately similar to XP_002275142.2 PREDICTED: two-component response regulator ARR1-like [Vitis vinifera].
2 1476 Les.9675 Transcribed locus, moderately similar to XP_002272710.1 PREDICTED: membrane-anchored ubiquitin-fold protein 4 [Vitis vinifera].
2 1476 Les.9672 Transcribed locus, weakly similar to NP_565011.1 auxin efflux carrier-like protein [Arabidopsis thaliana].
2 1476 Les.9670 Transcribed locus.
2 1476 Les.9621 Transcribed locus, moderately similar to NP_563986.1 NDH-dependent cyclic electron flow 1 [Arabidopsis thaliana].
2 1476 Les.9557 Transcribed locus, moderately similar to XP_002263700.1 PREDICTED: UDP-glycosyltransferase 75D1-like [Vitis vinifera].
2 1476 Les.9444 Transcribed locus, weakly similar to NP_001190416.1 uncharacterized protein [Arabidopsis thaliana].
2 1476 Les.9237 Transcribed locus, moderately similar to XP_002314782.1 predicted protein [Populus trichocarpa].
2 1476 Les.9204 Transcribed locus, strongly similar to NP_187956.1 TCP-1/cpn60 chaperonin family protein [Arabidopsis thaliana].
2 1476 Les.9172 Transcribed locus, moderately similar to XP_002267096.1 PREDICTED: uncharacterized protein LOC100257198 isoform 1 [Vitis vinifera].
2 1476 Les.9158 Transcribed locus, moderately similar to XP_002267563.2 PREDICTED: uncharacterized protein LOC100259729 [Vitis vinifera].
2 1476 Les.91 Nine-cis-epoxycarotenoid dioxygenase.
2 1476 Les.9050 Transcribed locus.
2 1476 Les.8741 Transcribed locus, moderately similar to XP_002272448.2 PREDICTED: uncharacterized protein LOC100253419 [Vitis vinifera].
2 1476 Les.8550 Transcribed locus, moderately similar to XP_001772347.1 predicted protein [Physcomitrella patens subsp. patens].
2 1476 Les.8505 Transcribed locus, moderately similar to XP_003632252.1 PREDICTED: nuclear cap-binding protein subunit 1-like isoform 2 [Vitis vinifera].
2 1476 Les.8386 Transcribed locus, moderately similar to XP_002269615.1 PREDICTED: S-type anion channel SLAH1 [Vitis vinifera].
2 1476 Les.8178 Transcribed locus, weakly similar to XP_003518622.1 PREDICTED: uncharacterized protein LOC100813734 [Glycine max].
2 1476 Les.8148 Transcribed locus, strongly similar to XP_002314056.1 predicted protein [Populus trichocarpa].
2 1476 Les.8063 Transcribed locus, moderately similar to NP_568534.1 armadillo/beta-catenin-like repeat-containing protein [Arabidopsis thaliana].
2 1476 Les.7899 Transcribed locus, weakly similar to XP_002300210.1 tir-nbs-lrr resistance protein [Populus trichocarpa].
2 1476 Les.7418 Transcribed locus, moderately similar to NP_001239965.1 uncharacterized protein LOC100802108 [Glycine max].
2 1476 Les.7308 Transcribed locus, moderately similar to NP_182099.1 putative methyltransferase PMT16 [Arabidopsis thaliana].
2 1476 Les.7198 Transcribed locus, moderately similar to NP_001049719.2 Os03g0277300 [Oryza sativa Japonica Group].
2 1476 Les.7145 Transcribed locus, moderately similar to NP_175576.1 ATP synthase subunit epsilon [Arabidopsis thaliana].

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Source: NCBI UniGene

EST Sequences

1,542 EST sequences from this library have been submitted to the public sequence database as of 02-Aug-2012.

Source: NCBI GenBank

Click the button to save sequences to a file (FASTA format)

Keywords

  • fruit
  • ripening
  • normalized

Source: NCBI Clone Registry



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